Urothelial cancer (UC) of the upper urinary tract (UTUC) accounts for 5-10% of UC.Despite sharing a common histology with bladder UC (UCB),staging & prognosis differences have been reported.To dissect the central biological features of UTUC driving its phenotype,we performed an integrated analysis of UTUC tumors using whole-exome (WES) & RNA sequencing (RNAseq).We compared the exome & transcriptome of UTUC to the TCGA UCB and an independent UTUC validation dataset (VALD).We performed an integrated analysis of WES (n=16) & RNAseq (n=19) from biobanked nephroureterectomy archival specimens of 19 chemotherapy-naïve patients with UTUC. Patients’ demographics are as follows:median age 71 (range 46-87);11 men,8 women;11 former/current smokers;13 renal pelvis,6 ureteral;17 high-grade,2 low-grade;8 low stage (=pT2).Our analyses revealed several insights:1) UTUC has a significantly lower frequency of TP53 mutations (3/16, 18.7%) compared to UCB patients (198/412, 48%) (p=0.03) but similar frequency of mutations in chromatin modifying (KMT2C, KMT2D, KDM6A), transcription activation (CREBBP), receptor tyrosine kinase (FGFR3, PIK3CA, ERBB2, KRAS), & cell cycle regulation (RB1) genes.2) UTUC is characterized by downregulation of the DNA mismatch repair genes (p=0.05) & APOBEC3A, APOBEC3B genes (p<0.01) & a lower total mutational burden compared to UCB (2 vs 5 mutations per Mb, p=0.01).3) UTUC is intrinsically non-basal. UTUC is predominantly luminal by UNC (18/19, 95%) & the MD Anderson (MDA) (17/19, 89%) criteria, and luminal-papillary (16/19, 84%) by the TCGA criteria. All VALD UTUC tumors (n=10) clustered with the luminal-papillary subtype.4) UTUC tumors exhibit a T-cell depleted phenotype (17/19, 89%). 5) FGFR3 expression is a dominant transcriptional outlier in UTUC (7/19, 37%) and is associated with T-cell depleted phenotype (p<0.01).By dissecting the biology of UTUC,we provide the biological rationale for future UTUC-specific therapeutic strategies.