5584 Background: Squamous cell carcinoma (SCC) represents <1% of all Ovarian cancers (OC) and is associated with poor prognosis. This study seeks to identify prognostic factors and molecular markers associated with OSCC compared to Endometrioid OC (EOC), Clear Cell OC (CCOC), HPV16/18-negative vulvar SCC (VSCC) and HPV16/18-negative cervical SCC (CSCC). Methods: 812 EOC, 846 CCOC, 32 OSCC, 15 malignant BT, 500 HPV16/18- CSCC, and 472 HPV16/18- VSC were analyzed using next-generation sequencing of DNA (NextSeq, 592 genes and NovaSeq, WES) and RNA (NovaSeq, WTS) (Caris Life Sciences, Phx, AZ). Tumor mutational burden (TMB) was measured by totaling all somatic mutations (mt) per tumor (TMB-H: > 10 mt/MB). PD-L1 IHC positivity was determined by a cut-off of >1% CPS (22c3, Agilent) and >2|5% (SP142, Spring Biosciences). HPV status determined by WES for HPV16 and 18. Statistical significance determined using chi-square and Mann-Whitney U test and adjusted for multiple comparisons (q<0.05). UMAP was used to visualize differences or similarities in transcriptomic profiles. Real-world overall survival (rwOS) obtained from insurance claims data and calculated from first treatment to last contact. Hazard ratio (HR) was calculated by Cox proportional hazards, with p-value calculated using log-rank test. Results: OSCC had the highest rate of TP53-mt and CDKN2A-mt compared to BT, EOC, CCOC, and CSCC (TP53-mt: 71.9%, 33.3%, 25.1%, 11.6% and 27.1%, CDKN2A-mt: 25%, 0%, 1.49%, 0.48%, and 4.45%) but lower than VSCC (TP53-mt: 80%, CDKN2A-mt: 38.9%). OSCC had lower mt of Chromatin Remodeling (CR) genes ARID1A (3.13%) compared to EOC (39.3%) and CCOC (58.2%) but higher mt of CR gene KMT2D (19.4%) compared to CCOC (3.62%) (q<0.05). OSCC had increased TMB-H than EOC, CCOC and VSCC (41.9% vs 13.6% vs 5.7% vs 8.84%) and PD-L1 IHC (all q<0.05). There was no ER/PR staining in OSCC. Median interferon (IFN) score was higher in OSCC compared to EOC, CCOC and BT (-0.24 vs -0.44 vs -0.46 vs -0.51, q<0.05) but similar to CSCC (-0.29) and VSCC (-0.17). Pathway analysis showed enrichment of IFNγ Response, Inflammatory Response, EMT and TNFα Signaling (NES: 1.53-2.05, FDR<0.25) in OSCC compared to EOC and CCOC. UMAP showed OSCC clustering more closely with CSCC and VSCC compared to EOC and CCOC. OSCC had worse post-Carboplatin survival (19.6 mo) compared to EOC (71.6 mo, p<0.01) and CCOC (46.9 mo, p<0.01), similar post-Carbo survival to TP53-mt CSCC (22.5 mo; p=0.80) but improved post-Carbo survival compared to TP53-mt VSCC (9.05 mo; p=0.01). Conclusions: The molecular and transcriptomic profile of OSCC is distinct from EOC, CCOC, and BT but similar to CSCC and VSCC. OSCC demonstrated a more immune hot phenotype. Further studies are needed to investigate the potential use of immunotherapy in OSCC.