EX-99.1

Enabling Next-Generation

Gene and Cell Therapies

JP Morgan Healthcare Conference Investor Presentation

January 2015

Exhibit 99.1

Forward-Looking Statements

Special Note Regarding Forward-Looking Statements

Some of the matters discussed in this presentation may constitute forward-looking statements within the meaning of the “safe harbor” provisions of

the Private Securities Litigation Reform Act of 1995. Forward-looking statements relate to expectations, beliefs, projections, future plans and strategies,

anticipated events or trends and similar expressions concerning matters that are not historical facts. The forward-looking statements are based on

Intrexon’s beliefs, assumptions and expectations of its future performance, taking into account all information currently available to it. These beliefs,

assumptions and expectations can change as a result of many possible events or factors, not all of which are known to Intrexon or are within its control.

The following factors, among others, could cause actual results to vary from the forward-looking statements: These risks and uncertainties include, but

are not limited to, (i) our ability to enter into new exclusive channel collaborations (ECCs) and joint ventures; (ii) developments concerning our existing

ECCs; (iii) competition from existing technologies and products or new technologies and products that may emerge; (iv) our ability, and the ability of

our collaborators, to protect our intellectual property and other proprietary rights and technologies; (v) the ability of our collaborators to secure any

necessary regulatory approvals to commercialize any products developed under the ECCs; (vi) the rate and degree of market acceptance of any

products developed by a collaborator under an ECC; and (vii) our expectations relating to AquaBounty and Trans Ova Genetics. Intrexon does not

undertake any obligation to update any forward-looking statements to reflect circumstances or events that occur after the date on which such

statements were made except as required by law. Additional information about factors affecting Intrexon is available in Intrexon’s Annual Report on

Form 10-K for the year ended December 31, 2013, and Quarterly Report on Form 10-Q for the period ended September 30, 2014, and other filings with

the SEC, which are available at www.sec.gov.

Use of Non-GAAP Financial Measures

This presentation presents Adjusted EBITDA and Pro Forma Adjusted EBITDA earnings per share, which are non-GAAP financial measures within the

meaning of applicable rules and regulations of the Securities and Exchange Commission (“SEC”). For a reconciliation of Adjusted EBITDA to net loss

attributable to Intrexon in accordance with generally accepted accounting principles and for a discussion of the reasons why the company believes that

these non-GAAP financial measures provide information that is useful to investors see the tables below under “Reconciliation of GAAP to Non-GAAP

Measures.” Such information is provided as additional information, not as an alternative to our consolidated financial statements presented in

accordance with GAAP, and is intended to enhance an overall understanding of our current financial performance.

© 2015 Intrexon Corp. All rights reserved. Intrexon Corporation is sharing the following materials for informational purposes only. Such materials do not constitute an offer to sell or the solicitation of an offer to

buy any securities of Intrexon. Any offer and sale of Intrexon’s securities will be made, if at all, only upon the registration and qualification of such securities under all applicable federal and state securities laws or

pursuant to an exemption from such requirements. The attached information has been prepared in good faith by Intrexon. However, Intrexon makes no representations or warranties as to the completeness or

accuracy of any such information. Any representations or warranties as to Intrexon shall be limited exclusively to any agreements that may be entered into by Intrexon and to such representations and warranties as

may arise under law upon distribution of any prospectus or similar offering document by Intrexon.

New Standard in Non-Viral Adoptive Cellular Therapies

Laurence J.N. Cooper, M.D., Ph.D., Professor of Pediatrics at MD

Anderson

Gregory Frost, Ph.D., Senior Vice President, Head of Intrexon’s Health Sector

Jonathan Lewis, M.D., Ph.D., Chief Executive Officer of ZIOPHARM

Oncology

Development of Non-Viral Adoptive Cellular Therapies for Cancer Treatment

ZIOPHARM presentation today at 3:30PM in California West Room;

Breakout Session in Olympic Room at 4:00PM

What would it take for a

disruptive new platform to

eclipse >$20B/year

in sales of anti-cancer

monoclonal antibodies?

immunologically tolerated

scalable

manufacturing

target specificity

efficacy

ADC’s

ADCC

bi-specific

modular framework

2013 Worldwide mAb anti-cancer sales: FiercePharma

Unprecedented Efficacy

Pre-Treatment

Diagnosis CLL

Estimated Tumor Burden >2 kg

Post-Treatment

No evidence of CLL

(by histology, FACS, cytogenetics FISH and

deep sequencing)

NEJM. (2011) 365(8): 725–733

That Is Durable

No Evidence

of Disease

> 24mos

NEJM.

(2014) 371: 1507-1517

Adoptive Cell Therapy Has Shown Impressive Early Signs of Efficacy

NEJM. (2014)

371: 1507-1517

Yet ON Target Toxicity Is A MAJOR Issue For MANY Targets

J Clin Oncol. (2006) 24:e20–2

If Adoptive Cellular Therapy Cannot Be Controlled…

Reassessing target antigens for adoptive T-cell therapy

…its application will be severely limited

Nature Biotechnology. (2013) 31:999-1008

And If CARs Cannot Be Manufactured In A Scalable Fashion…

…they will remain as local ‘therapies’

instead of global solutions

Blood. (2011) 118(18):4761-4762

Intrexon’s Vision of Synthetic Immunology

Nature 487: 64-69.

Molecular rewiring of immunologic circuitry in

cellular products through synthetic multigenic programs to

generate safe and highly-effective oncolytic effectors

Intrexon Is Building The Solutions For CAR-T Cell Therapies

Intrexon has the integrated technology platforms to actualize the potential of

CAR-T

Cell

therapies.

Utilization

our

RheoSwitch

facilitates

exquisite

regulation

of multiple bioeffectors in CAR-T Cells enabling physicians to control systemic

effects of cell therapies by delivering minimally invasive oral activator ligands.

UltraCART Value Drivers

RHEOSWITCH

MULTIGENIC

ATTSITE

RECOMBINASES

FULLY HUMAN

CAR DISCOVERY

COMBI-CAR DEV.

PROGRAM

ALLOGENEIC T-

CELL PLATFORM

IMPLEMENTATION TOWARD MULTIPLE PRODUCTS

ENABLING APPLICATIONS (IN DEVELOPMENT)

IMPROVED

SAFETY

IMPROVED

EFFICACY

IMPROVED

MANUFACTURING

Intrexon –

ZIOPHARM -

MDACC Collaboration

Registration Trials & Global Distribution

with Multiple Pharma Partners

•

Candidate Generation

•

Product Refinement

•

Clinical POC

•

Single Center

Translational Trials of

Novel Prototypes

Dual Approach to Identify Most Effective CAR-T Products

•

Point of Care Controlled

pDNA CAR-T/TCR Design

Universal Donor Cell

Substrate Development

•

Translational Medicine

•

Multicenter Trial Validation

ZIOPHARM

Oncology

ZIOPHARM

Oncology

Technology

Intrexon / ZIOPHARM / MD Anderson

RheoSwitch Therapeutic

System®

Most advanced family of ligands and switches available for

dynamic range, safety, and spatial/temporal control

Non-Viral

Integration Platform

First in-human testing of Sleeping Beauty system

in hematopoietic cells

UltraVector®

Industrialized assembly and screening of multigenic DNA

modules for synthetic biology

Adoptive Cell Therapy

Expertise in development and implementation of novel

immunotherapy trials

Laser-enabled Analysis and

Processing (LEAP®)

Computerized image-based selection and laser processing for

cell identification and purification

AttSite®

Recombinases

Stable, targeted gene integration and expression with

proprietary serine recombinases

Key Technology Synergies

Established

clinical

pipeline

for

adoptive

cellular

therapies

2015

and

beyond

Controlling Gene Expression with RheoSwitch®

(RTS®) Platform

•

RTS®

platform provides transcriptional control of a broad, diverse range of

therapeutic

genes

enabling

application

across

many

indications

•

RTS®

modulates protein expression and allows for repeated inducibility

•

Clinically validated with excellent safety profile

•

Highly controllable dose-dependent gene expression demonstrated both ex vivo

and in vivo

•

RheoPlex

switches

provide

independent

control

over

multiple

genes

within

single cell

RTS®

Activator Ligand

Administered Orally

RTS®

Conditional Delivery Of Distinct Immune Effectors

RTS

has shown conditional delivery

of immune effectors in a single vector

IFN

IL-12

p70

CTLA-

4 DCY

IFN

IL-12

CTLA-4 DCY

pg/mL

Uninduced

Induced

Uninduced

Induced

Uninduced

Induced

100

200

300

2000

4000

6000

2000

4000

6000

Tissue Specific Cells

25000

20000

15000

10000

5000

Ubiquitous

Promoters

Tissue Specific

Promoters

Non-Tissue Specific Cells

Ubiquitous

Promoters

Tissue Specific

Promoters

16000

12000

8000

4000

No Expression

RTS®

Spatial and Temporal Expression

RTS

system can be tailored for

cell type and state specific spatial regulation

Features of the AttSite®

Recombinase System

•

Library

of AttSite®

characterized serine

recombinases

•

Unidirectional

stable integration

technology (unlike cre/lox)

•

Targeted

gene delivery to pre-

positioned AttSites in the genome

•

Allows

long-term

and

stable

gene

expression from AttSites

•

Specific targeting to a finite number of

pseudosites

(imperfect

recognition

sites) in the genome

AttSite®

Recombinase

Technology

Precision

Control

Safety

Pseudo AttSite®

Recombinase

Mediated Stable Integration

AttSite®

recombinases

facilitate

integration

intact transgenes at low copy number into a finite

number

pseudo

AttSites®

the

genome.

One

hundred percent transgene integrity and 1-6

integrations per cell have been achieved.

DNA sequence can be cloned between terminal

inverted repeats (TIR) of the transposon and then

mobilized into TTAA chromosomal sites by the

transposase. System can generate insertions in

the range of 1-50 copies per cell depending on

dosage of the transfected plasmids.

Transposon Mediated Stable

Integration

Non-Viral Integration Platform for Large Payloads

Nature Protocols. (2011) 6:1521-1535

Transposon

binds to vector

Excision and

integration

Chromosome

attP

attR

+ recombinase

Irreversible

integration

attL

Chromosome

attB

Plasmid

Intrexon’s Multi-Horizon Strategy of Synthetic Immunology

Build

Test

Learn

Design

Build

Test

Learn

Design

Build

Test

Learn

Design

Autologous

Allograft

Immortalized

Universal Donor

CAR/TCR-T

GM-DC

UltraCART

GM-ERC/NK

Intrexon Empowering Broad Gene and Cell Therapy Applications

GM Cell Delivery

RTS®

Based Expression Control

Cell Therapy

Applications

Utilizing

Intrexon

Technology

Rare Disease:

Friedreich’s

Ataxia

Oncology:

Autologous

Approach

Oncology:

Allogeneic

Platforms

Ocular Disease:

Age-related

Macular

Degeneration

Cartilage Repair:

Allogeneic

Chondrocyte

Cells

Rare Skin

Disorders:

RDEB

Human

Infertility:

In Vitro Egg

Maturation

Activator Ligand

Delivery via Pill or

Eye Drops

Gene of Interest

Activator Ligand

Protein of Interest

RTS

Platform For Controlled

Ocular Expression

Gene-based Therapies for Ocular Diseases Utilizing RTS®

•

Current approaches to chronic ocular

diseases require intraocular delivery

with repeated injections for

sustained therapeutic distribution

•

JV with Sun Pharma developing gene

therapies for treatment of ocular

diseases causing partial or total

blindness

•

Use of RTS

platform with activator

ligand will enable patients to receive

a targeted biologic therapy without

having to endure frequent injections

•

Initial target is age-related macular

degeneration

GOI

Cell-based Treatments for Rare Skin Diseases

•

Collaboration with Fibrocell Science to

develop genetically-modified human

dermal fibroblasts expressing collagen

VII for treatment of Recessive

Dystrophic Epidermolysis Bullosa (RDEB)

•

RDEB has no approved treatment and is

often lethal before the age of 30

•

Plan to file an IND application with the

U.S. FDA in 1H of 2015 for drug

candidate, GM-HDF-COL7

•

Also pursuing Linear scleroderma, a

skin-hardening disease affecting

movement and development

Intrexon in 2015

Continued Expansion Into New Fields

Intrexon Fields of Collaboration

2011

2012

2013

2014

Energy

Environment

Consumer

Food

Health

Cell

Engineering

Molecular

Engineering

Organ & Organism

Engineering

Synthetic Biology

Integrating through Collaboration into Industrial Leadership

Energy

Consumer

Health

Environment

Food

Gene & Cell

Therapies

Animal

Cloning

Bovine

Embryos

Research

Animal Models

GM Food

Animals

Increasing Capital Efficiency to Unburden Product Economics

$10

$15

$20

$25

Q1 2013

Q2 2013

Q3 2013

Q4 2013

Q1 2014

Q2 2014

Q3 2014

Revenues (in millions)

20%

40%

60%

80%

FY 2013

Q3 2013

Q4 2013

Q1 2014

Q2 2014

Q3 2014

Cost Recovery as % of Cash OpEx

FY2013 & Past 4 Quarters

Lead the Second

Generation of Biotech

Increase Portfolio

of Backend Economics

Increase Deal

Money

Increase Cost

Recovery

50%

100%

150%

FY2012

FY2013

FY 2014 (9 mos)

Cost Recovery & Deal Money as %

of Cash OpEx

FY2012, FY2013, FY2014 (9 months)

THANK

YOU!

Appendix A

Intrexon Corporation and Subsidiaries

Reconciliation of GAAP to Non-GAAP Measures (Unaudited)

Adjusted EBITDA.

reconciliation of Adjusted EBITDA to Intrexon's net income or loss attributable to Intrexon under GAAP appears below. Adjusted EBITDA is a non-GAAP financial measure that Intrexon calculates

as net income or loss attributable to Intrexon adjusted for income tax expense or benefit, interest expense, depreciation and amortization, stock-based compensation, contribution of services by

shareholder, unrealized appreciation or depreciation in the fair value of equity securities, gain on previously held equity investment, equity in net loss of affiliate and the change in deferred revenue

related to upfront and milestone payments. Adjusted EBITDA is a key metric for Intrexon's management and Board of Directors for evaluating the Company's financial and operating performance,

generating future operating plans and making strategic decisions about the allocation of capital. Management and the Board of Directors believe that adjusted EBITDA is useful to understand the long-

term performance of Intrexon's core business and facilitates comparisons of the Company's operating results over multiple reporting periods. Intrexon is providing this information to investors and

others to assist them in understanding and evaluating the Company's operating results in the same manner as its management and board of directors. While Intrexon believes that this non-GAAP

financial measure is useful in evaluating its business, and may be of use to investors, this information should be considered as supplemental in nature and is not meant as a substitute for the related

financial information prepared in accordance with GAAP. In addition, this non-GAAP financial measure may not be the same as non-GAAP financial measures presented by other companies. Adjusted

EBITDA is not a measure of financial performance under GAAP, and is not intended to represent cash flows from operations under GAAP and should not be used as an alternative to net income or loss

as an indicator of operating performance or to represent cash flows from operating, investing or financing activities as a measure of liquidity. Intrexon compensates for the limitations of Adjusted

EBITDA by using it only to supplement the Company's GAAP results to provide a more complete understanding of the factors and trends affecting the Company's business. Adjusted EBITDA has its

limitations as an analytical tool and you should not consider it in isolation or as a substitute for analysis of Intrexon's results as reported under GAAP.

In addition to the reasons stated above, which are generally applicable to each of the items Intrexon excludes from its non-GAAP financial measure, Intrexon believes it is appropriate to exclude certain

items for the following reasons: Interest expense may be subject to changes in interest rates which are beyond Intrexon's control; Depreciation of Intrexon's property and equipment and amortization of

acquired identifiable intangibles can be affected by the timing and magnitude of business combinations and capital asset purchases; Stock-based compensation expense is a noncash expense and may

vary significantly based on the timing, size and nature of awards granted and also because the value is determined using formulas which incorporate variables, such as market volatility; Contribution of

services by shareholder is a noncash expense which Intrexon excludes in evaluating its financial and operating performance; Unrealized appreciation or depreciation in the fair value of securities which

Intrexon holds in its collaborators may be significantly impacted by market volatility and other factors which are outside of the Company's control in the short term and Intrexon intends to hold these

securities over the long term; Equity in net loss of affiliate reflects Intrexon's proportionate share of the income or loss of entities over which the Company has significant influence, but not control, and

accounts for using the equity method of accounting. Gain on previously held equity investment occurred as a result of a step acquisition of AquaBounty Technologies, Inc. which was completed in the

first quarter of 2013 which resulted in a controlling interest by Intrexon and the consolidation of the investment. Intrexon believes excluding the impact of such losses or gains on these types of strategic

investments from its operating results is important to facilitate comparisons between periods; and GAAP requires Intrexon to account for its collaborations as multiple-element arrangements. As a

result, the Company defers certain collaboration revenues because certain of its performance obligations cannot be separated and must be accounted for as one unit of accounting. The collaboration

revenues that Intrexon so defers arise from upfront and milestone payments received from the Company's collaborators, which Intrexon recognizes over the future performance period even though the

Company's right to such consideration is neither contingent on the results of Intrexon's future performance nor refundable in the event of nonperformance. In order to evaluate Intrexon's operating

performance, its management adjusts for the impact of the change in deferred revenue for these upfront and milestone payments in order to include them as a part of adjusted EBITDA when the

transaction is initially recorded. The adjustment for the change in deferred revenue removes the noncash revenue recognized during the period and includes the cash and stock received from

collaborators for upfront and milestone payments during the period. Intrexon believes that adjusting for the impact of the change in deferred revenue in this manner is important since it permits the

Company to make quarterly and annual comparisons of the Company's ability to consummate new collaborations or to achieve significant milestones with existing collaborators. Further, Intrexon

believes it is useful when evaluating its financial and operating performance, generating future operating plans and making strategic decisions about the allocation of capital.

Pro forma adjusted EBITDA per share. Intrexon's calculations for pro forma adjusted EBITDA per share, basic and diluted, assumes, as of the end of the respective period, the conversion of all

outstanding shares of Intrexon's redeemable convertible preferred stock plus all cumulative dividends payable thereon into shares of common stock as if such conversion had occurred as of the

later of (i) the beginning of the period or (ii) the issuance date of those shares. Because all of Intrexon's shares of redeemable convertible preferred stock and all accrued and cumulative

dividends thereon automatically converted into common shares upon the closing of the Company's initial public offering on August 13, 2013, Intrexon believes that the inclusion of such shares

on an as-converted basis results in a useful metric for its investors, analysts and others when evaluating Intrexon's results on a comparable basis with other periods. While Intrexon's management

and board of directors believe that this non-GAAP per share metric is useful in evaluating the Company's past adjusted EBITDA results, and may be of use to investors, analysts and others, this

information should be considered supplemental in nature and is not meant as a substitute for the per share information prepared in accordance with GAAP. In addition, this non-GAAP per share

metric may not be the same as non-GAAP per share metrics presented by other companies. Pro forma adjusted EBITDA per share is not a measure of financial performance under GAAP, and is

not intended to represent cash flows per share from operations under GAAP and should not be used as an alternative to net income or loss per share as an indicator of operating performance or to

represent cash flows from operating, investing or financing activities as a measure of liquidity. Intrexon compensates for the limitations of pro forma adjusted EBITDA per share by using it only

to supplement the Company's GAAP results to provide a more complete understanding of the factors and trends affecting the Company's business. Pro forma adjusted EBITDA per share has its

limitations as an analytical tool and you should not consider it in isolation or as a substitute for analysis of Intrexon's results as reported under GAAP.

Continued on next slide…

To supplement Intrexon's financial information presented in accordance with U.S. generally accepted accounting principles ("GAAP"), Intrexon presents Adjusted EBITDA. A

Appendix A continued

(1) Pro forma adjusted EBITDA per share,

basic and diluted have been calculated for

the three and nine month periods ended

September 30, 2013 after giving effect to

(i) the conversion of 112,906,464 shares

of Intrexon's preferred stock outstanding

on January 1, 2013 into 64,517,977 shares

of common stock upon the completion of

its initial public offering; (ii) the issuance

of 19,047,619 shares of Series F preferred

stock issued between January 1, 2013 and

April 30, 2013 and the conversion of those

shares into 10,884,353 shares of Intrexon's

common stock upon the completion of its

initial public offering; and (iii) upon the

completion of Intrexon's initial public

offering the conversion of aggregate

cumulative dividends on the Company's

preferred stock of $68.8 million into

4,302,800 shares of its common stock at

the initial public offering price of $16.00

per share.

The following table presents a reconciliation of net income (loss) attributable to Intrexon to EBITDA and also to adjusted

EBITDA for each of the periods indicated:

Three months ended

Nine months ended

September 30,

2014

2013

2014

2013

(In thousands, except share and per share data)

Pro forma adjusted EBITDA per share:

Numerator:

Adjusted EBITDA

1,594

(5,034)

8,754

(16,576)

Denominator (1):

Pro forma weighted average common shares

used in computing pro forma adjusted EBITDA

per share, basic

99,888,203

91,558,838

98,711,564

83,738,327

Pro forma weighted average common shares

used in computing pro forma adjusted EBITDA

per share, diluted

101,487,136

91,558,838

100,497,766

83,738,327

Pro forma adjusted EBITDA per share, basic

0.02

(0.05)

0.09

(0.20)

Pro forma adjusted EBITDA per share, diluted

0.02

(0.05)

0.09

(0.20)

The following table presents the calculation of pro forma adjusted EBITDA per share, basic and diluted, for each of the

periods indicated:

Three months ended

Nine months ended

September 30,

2014

2013

2014

2013

(In thousands)

Net income (loss) attributable to Intrexon

(52,725)

15,498

(100,653)

(26,776)

Interest expense

210

258

Income tax expense

—

Depreciation and amortization

2,970

1,748

6,681

5,421

EBITDA

(49,545)

17,252

(93,691)

(21,325)

Stock-based compensation expense

4,213

633

14,770

1,828

Contribution of services by shareholder

508

388

1,485

1,163

Unrealized (appreciation) depreciation in fair

value of equity securities

37,089

(27,339)

48,944

(5,704)

Gain on previously held equity investment

—

(7,415)

Equity in net loss of affiliates

1,619

—

3,510

390

Impact of change in deferred revenue related

to upfront and milestone payments

7,710

4,032

33,736

14,487

Adjusted EBITDA

1,594

(5,034)

8,754

(16,576)