Abstract Background: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare, highly aggressive form of ovarian cancer primarily diagnosed in young women. The molecular basis of this disease is unknown, and there are limited therapeutic options. The tissue of origin remains speculative, and SCCOHT is still categorized as a miscellaneous tumor by the World Health Organization. Methods: We performed target capture and massively parallel DNA sequencing to a mean depth 442x across 279 key cancer-associated genes in 12 SCCOHT samples. All mutations were validated using orthogonal techniques and their somatic nature was determined by sequencing matched germline DNA. Mutation expression and the consequence of splice site variants were determined through RNA sequencing. Protein expression was determined through immunoblotting and immunohistochemistry. Functional significance was determined through in vitro manipulation using over-expression and knockdown constructs. Results: All 12 patients (median age 26.5 yrs; range 18-42 yrs) had inactivating bi-allelic variants in the chromatin regulator SMARCA4, including splice site, nonsense, and frameshift mutations or exon deletions. One patient had a germline mutation with somatic loss of the wild-type allele. All mutations were detected in RNA transcripts, and splice site variants resulted in transcribed introns. Immunoblotting and immunohistochemistry confirmed loss of SMARCA4 protein expression in 7 of 9 cases with mutations and available tissue. SMARCA4 somatic mutations were more common in SCCOHT than other solid tumors found in The Cancer Genome Atlas (p < 2.22 x 10-16). Ectopic re-introduction of SMARCA4 resulted in a dose-dependent suppression of cell growth and an expected increase in p21. Stable depletion of SMARCA4 using lentiviral expressed short hairpin RNA led to an increase in cell growth as measured by an XTT proliferation assay. Conclusions: SMARCA4 SWI/SNF chromatin-remodeling complex mutations were uniformly identified in all SCCOHT examined. The SCCOHT tumors had few other mutations in the panel of sequenced genes. The inactivating mutations are infrequently mutated in other solid tumors and are consistent with the characteristics of a tumor suppressor. Most of the identified mutations reside within the known helicase catalytic domains of SMARCA4, suggesting a role in tumorigenesis. One case contained a germline mutation, which is consistent with prior reports suggesting a hereditary component to this disease. These data suggest that canonical mutations in SMARCA4 are an important therapeutic target for further investigation. Citation Format: Petar Jelinic, Jennifer Mueller, Narciso Olvera, Fanny Dao, Sasinya N. Scott, Ronak Shah, JianJiong Gao, Nikolaus Schultz, Mithat Gonen, Robert A. Soslow, Michael F. Berger, Douglas A. Levine. SMARCA4 mutations in small cell carcinoma of the ovary. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-91. doi:10.1158/1538-7445.AM2014-LB-91