Background: Upper tract urothelial carcinoma (UTUC) represents up to 10% of all urothelial carcinoma (UC). UTUC is a lethal malignancy, with nearly one half the patients dying within 5 years. Our objective was to understand the biological differences between UTUC and bladder UC.Methods: Fresh frozen chemotherapy-naïve primary tumors from nephroureterectomy cases and corresponding germline samples underwent whole exome sequencing (WES) and RNA sequencing (RNAseq). The Cancer Genome Atlas (TCGA) WES and RNAseq raw data was reanalyzed through our in-house bioinformatic pipeline to compare the mutational and transcriptomic landscape of UTUC to bladder UC. We evaluated the expression values for a set of 40 housekeeping genes between the two different datasets to exclude batch effects. We used gene set Enrichment Analysis (GSEA) to identify differentially enriched pathways in UTUC.Results: 17 tumors underwent WES, 20 RNAseq, with 11 analyzed for both WES and RNAseq. UTUC samples harbored several recurrent mutations including PIK3CA (4/17), FGFR3 (2/17), MLL2 (4/17), MLL3 (2/17), ATM 2/17). Three KRAS mutations were discovered in two patients (G12D, G12V and Q61H), which were confirmed by targeted sequencing. Frequent copy number alterations included CDKN2A/B deletions (3/17), BG4ALT3, SEMG1 and USP6 amplifications (2/17 each). GSEA analysis revealed significant enrichment of the KRAS signaling in UTUC whereas bladder UC showed an enrichment of genes involved in mTOR and E2F signaling. There were significant differences in the expression of several key DNA damage repair (DDR) pathway genes between the two entities including TP53, RAD51 and ERCC4 despite infrequent or absent mutations in these genes (q value 0.03 for DDR gene set). MSH5, a gene associated with cisplatin-resistance was the most highly ranked DDR overexpressed gene in UTUC compared to bladder UC (enrichment score = 0.8).Conclusions: This study generates a detailed genomic and transcriptomic profile of UTUC. RNAseq demonstrated a distinct pattern of DDR pathway expression in UTUC independent of genomic alterations; these findings may have important implications for platinum-based chemotherapy.