This presentation contains certain forward looking information about ZIOPHARM Oncology that is intended to be covered by the safe harbor for forward looking statements provided by the Private Securities Litigation Reform

Chimeric Antigen Receptor (CAR+) T cells: Target cell surface tumor associated antigens (TAAs) independent of HLA Public antigens 2. T Cell Receptor (TCR + ) cells: Target intracellular TAAs dependent on HLA Private antigens 3. Natural Killer (NK) cells: Target tumor with loss of HLA No antigens 12 Improving the Therapeutic Potential of CAR T Understanding of the effector cell biology Co stimulation with cytokine Signals 1 2 Signal 3 13 Advantages of Non Viral Gene Integration Sleeping Beauty transposon/transposase system Fast, efficient and nimble gene transfer method Improves cost, time, and complexity compared to viral based integration 14 Management of Potential Toxicity through Inducible Immunoreceptor Expression ( in vivo control) Many attractive target antigens are also expressed on normal cells Inducible CAR + T Cell Inducible TCR + T Cell CAR + T Cell TCR + T Cell 15 Veledimex Next Generation Building the Next Generation of Inducible Cytokines ( in vivo control) Therapeutic potential of effector cells depends on recognition of tumor cells and recycling effector function in tumor microenvironment. 16 Veledimex Next Generation IL 12 Cell Therapy Zhang, Rosenberg et al., Feb 2015, Clinical Cancer Research Tumor Infiltrating Lymphocytes Genetically Engineered with an Inducible Gene Encoding Interleukin 12 for the Immunotherapy of Metastatic Melanoma TIL plus IL 12 can mediate objective responses in up to 70% of patients with metastatic melanoma Enhances the activity of effector CD4+ and CD8+ T cells as well as natural killer NK and NK T cells Collapse of tumor stroma is triggered by IL 12 induction of Fas* 50 to 100 fold fewer cells compared to standard TIL protocols and in the absence of IL 2 co administration Transferred cells did not persist long term and were associated with severe dose limiting toxicity * Kerkar, Rosenberg et al., Mol Ther. 2013 Jul;21(7):1369 77 17 Next generation CAR + T cells Bioprocessing Close system Ex vivo cytokines Cryopreservation CAR design Humanization Stalk Endodomains Cytokine IL 12 Others Time in culture 0 30 days 18 New CD 19 CAR Design Using Sleeping Beauty Prior Sleeping Beauty CAR Design Modified 1 Sleeping Beauty CAR Design T cell infusion (day 1) Next generation design demonstrates superior in vivo activity in pre clinical models Established Disease Model Minimal Residual Disease Model T cell infusion (day 6) Prior Sleeping Beauty CAR Design Modified 1 Sleeping Beauty CAR Design 19 Cytokine Signaling Enhances CARs Persisting T cell Subsets ( in vitro ): Established Disease Model 20 CD95 Expression: + + + + Memory Subset: SCM CM EM EMRA CD19 specific CAR + T cells Template for CAR + T cells Safety Nearing completion Efficacy New CAR Efficacy POC OTS Generate in advance of need 21 Dual CMC Distribution Approaches for Cell Therapies Registration Trials Global Distribution with Multiple Pharma Partners Centralized Point of care (POC) Genetically modified T cells One patient Multiple Patients Autologous T cells Allogeneic T cells Real time In advance of need 22 Self Months Months Weeks Weeks Days Days Hours Hours T cell manufacturing time T cell acquisition Genetic modification Infusion Steps Toward Point of Care Distribution 23 Off the Shelf (OTS) Solution 24 Safely infuse patients No immediate or late toxicity No excess GVHD Outpatient infusions 50% of patients with aggressive disease remain in remission after transplant CAR + T cells Safely re infuse CAR + T cells from patient specific cryopreserved banks (n=3 re treated) CAR + T cells apparently effective in the adjuvant disease setting Approximately 28 day CAR + T cell persistence Ongoing Phase 1 Safety Study: First Generation Proof of Concept N = 16 pts treated, 8 remain in CR with median 7.5 mo. follow up Kebriaei et. al, EHA 2015 25 Future of T cell therapy 26 Drive Pipeline Forward To Create Value How Are We Differentiated Translation of immunology to immunotherapies T cells NK cells Non viral gene transfer (personalized therapies) CAR TCR Cytokine Cellular engineering Expression Control 27 Personalized and orally controlled cytokine transcription CAR + T cells Ad RTS IL 12 Differentiated Technology Platforms Lower cost, controllable toxicity, autologous and allogeneic 28 Technology Intrexon / ZIOPHARM / MD Anderson RheoSwitch Therapeutic System Most advanced family of ligands and switches available for dynamic range, safety, and temporal control (on off on etc.) 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 Personalized Therapy for Disease and Patient Infuse T cells with more than one specificity Personalized for the disease Intra tumor Inter tumor Heterogeneity of tumor associated antigen (TAA) Infuse T cells with one or more specificity Personalized for the patient N=1 trial paradigm 29 Power Law Curve The New Industrialization of T cells 30 The N=1 approach has been shown for non genetically modified T cells 31 www.ziopharm.com The Future of Cancer Therapy

Our audience is cautioned not to place undue reliance on these forward looking statements that speak only as of the date hereof, and we do not undertake any obligation to revise and disseminate forward looking statements to reflect events or circumstances after the date hereof, or to reflect the occurrence of or non occurrence of any events. 1 Forward Looking Statements Financial Highlights NASDAQ symbol ZIOP Approximately 128.2 million shares outstanding Cash and cash equivalents of approximately $129.7 million Cash resources sufficient to fund our operations into 2Q 2017 Excludes 2Q payment of $57.5 million from Intrexon related to the biopharmaceutical business of Merck KGaA agreement No debt * As of March 31, 2015 2 Intrexon and ZIOPHARM Collaboration with the Biopharmaceutical Business of Merck KGaA Highlights Significant Value of CAR T Platform 3 Exclusive strategic collaboration and license agreement to develop and commercialize CAR T cancer therapies Exclusive access to CAR T suite of technologies, including MD Anderson technologies Intrexon and ZIOPHARM responsible for all platform and product developments until IND filing Biopharmaceutical business of Merck KGaA to nominate targets of interest, lead IND filing and pre IND interactions, clinical development and commercialization Intrexon and ZIOPHARM retain ability to explore targets independently, granting Merck KGaA opt in rights during clinical development Up to $941M for two targets recognizes value of CAR T programs and technology, de risks portfolio and adds significant global development expertise Upfront, milestone and royalty payments divided evenly between ZIOPHARM and Intrexon Upfront payment of $115 million For the first two targets, up to $826 million development, regulatory and commercial milestones ($413 million per product) Tiered royalties up to lower double digits on net sales Merck KGaA may elect additional targets at additional cost Key Investment Highlights Robust synthetic immunology pipeline targeting hematologic malignancies and solid tumors Non viral and viral CAR T, TCR, and NK cell therapies IL 12 gene therapy: adenoviral vector for IL 12 expression controlled via oral activator Differentiated technology platforms In vivo control of gene expression by oral pill Non viral: faster and less complex lower cost Dual approach: Point of Care (autologous) Off the Shelf (allogeneic) Agreement with biopharmaceutical business of Merck KGaA: to elect initial 2 CAR T targets Multiple trial launches in 2015/2016 with potential data in Q4 2015 Well capitalized 4 Milestones 2015 / 2016 Intra tumoral IL 12 RheoSwitch Phase 1/2 Breast Cancer with SOC initiated Q2 2015 Phase 1 GBM initiated Q2 2015 potential early data Q4 2015 CAR T Initiate Phase 1 next generation CD19 CAR trials Potential early data on Phase 1 CARs studies in Q4 2015 Initiate novel CAR for myeloid malignancies in late 2015/early 2016 Other Leukemia and Solid Tumor CAR T trials in 2016 Allogenic, Off the Shelf T Cell Studies in 2016 5 Overall strategy and differentiation 6 Robust Pipeline In Synthetic Immunology Compound Pre Clinical Phase 1 Phase 2 Ad RTS IL 12 gene Rx IND Breast GBM Adoptive Cell Therapies B cell Malignancies Myeloid Malignancies RTS controlled T cell Solid Tumors Universal Donor 7 IL 12 Gene Therapy Adenoviral vector engineered to express IL 12 utilizing RheoSwitch Therapeutic System gene switch Injected intra tumor with IL 12 expression controlled via administration of oral activator ligand veledimex Regulated intra tumoral expression of IL 12 promotes activation of tumor infiltrating lymphocytes to drive cytotoxic immune response against distant tumors 8 Ad RTS IL 12 Oral Veledimex Precisely Controls Expression of IL 12 ( in vivo control) 9 Improved persistence and survival in tumor microenvironment Limits on target, off tumor toxicities Phase 1b/2 Study of IL 12 Gene Therapy in Locally Advanced/Metastatic Breast Cancer Immunotherapy phase of treatment A single cycle of Ad RTS hIL 12 + veledimex goal of maintaining or improving pre study response 1 O : Safety and tolerability 2 O : ORR, disease control and biomarkers Immunotherapy phase of treatment A single cycle of Ad RTS hIL 12 + veledimex goal of maintaining or improving pre study response 1 O : Safety and tolerability 2 O : ORR, disease control and biomarkers N = 40 locally advanced or metastatic breast cancer of all subtypes up to 20% (8 subjects) with HER2+ breast cancer Response (PR or SD) to first or second line standard therapy N = 40 locally advanced or metastatic breast cancer of all subtypes up to 20% (8 subjects) with HER2+ breast cancer Response (PR or SD) to first or second line standard therapy Suspend chemotherapy phase of treatment (HER2 therapy permitted) Suspend chemotherapy phase of treatment (HER2 therapy permitted) 10 Phase 1 Study of IL 12 Gene Therapy in Recurrent or Progressive Glioblastoma/Gr.III Malignant Glioma A single cycle of Ad RTS hIL 12 + escalating veledimex 1 O : Safety and tolerability 2 O : Determine MTD and immune response, including ORR, PFS and OS A single cycle of Ad RTS hIL 12 + escalating veledimex 1 O : Safety and tolerability 2 O : Determine MTD and immune response, including ORR, PFS and OS N = 72 Recurrent or progressive glioblastoma or Grade III malignant glioma Stratified according to clinical indication for tumor resection: Resection plus injection vs. stereotactic injection alone N = 72 Recurrent or progressive glioblastoma or Grade III malignant glioma Stratified according to clinical indication for tumor resection: Resection plus injection vs. stereotactic injection alone 11 Cell Therapy Portfolio of Effector Cells 1.

Food and Drug Administration or equivalent foreign regulatory agencies and for which indications; whether any of our therapeutic candidates will be successfully marketed if approved; whether our DNA based biotherapeutics discovery and development efforts will be successful; our ability to achieve the results contemplated by our collaboration agreements; the strength and enforceability of our intellectual property rights; competition from pharmaceutical and biotechnology companies; the development of and our ability to take advantage of the market for DNA based biotherapeutics; our ability to raise additional capital to fund our operations on terms acceptable to us; general economic conditions; and the other risk factors contained in our periodic and interim reports filed with the SEC including, but not limited to, our annual report on Form 10 K for the fiscal year ended December 31, 2014 and other filings with the SEC, which are available at www.sec.gov.

All of such statements are subject to certain risks and uncertainties, many of which are difficult to predict and generally beyond the control of the Company, that could cause actual results to differ materially from those expressed in, or implied or projected by, the forward looking information and statements. These risks and uncertainties include, but are not limited to: whether any of our therapeutic candidates will advance further in the clinical trials process and whether and when, if at all, they will receive final approval from the U.S.

Words such as expect(s), feel(s), believe(s), will, may, anticipate(s) and similar expressions are intended to identify forward looking statements. These statements include, but are not limited to, statements regarding our ability to successfully develop and commercialize our therapeutic products, our ability to expand our long term business opportunities; financial projections and estimates and their underlying assumptions; and future performance.

June 2015 www.ziopharm.com The Future of Cancer Therapy Exhibit 99.1 This presentation contains certain forward looking information about ZIOPHARM Oncology that is intended to be covered by the safe harbor for forward looking statements provided by the Private Securities Litigation Reform Act of 1995, as amended. Forward looking statements are statements that are not historical facts.