Background: 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 and prognosis differences have been reported. Methods: To dissect the central biological features of UTUC driving its phenotype, we performed an integrated analysis of UTUC tumors using whole-exome (WES) and RNA sequencing (RNAseq). We compared the exome and transcriptome of UTUC to the TCGA UCB and an independent UTUC validation dataset (VALD). Results: We performed an integrated analysis of WES (n = 16) and 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), 11 high 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), and cell cycle regulation (RB1) genes. 2) UTUC is characterized by downregulation of the DNA mismatch repair genes (p ≤ 0.05) and APOBEC3A, APOBEC3B genes (p < 0.01) and 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%) and 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 a T-cell depleted phenotype (p < 0.01). Conclusions: Our study demonstrates that UTUC is predominantly and intrinsically non-basal. We show that UTUC is characterized by a T-cell-depleted phenotype associated with FGFR3 overexpression. By dissecting the biology of UTUC, we provide the biological rationale for future UTUC-specific therapeutic strategies.