Background: Chromophobe renal cell carcinoma (chRCC) is a histologically and molecularly distinct class of rare renal cancer representing less than 5% of the kidney tumors. Molecular knowledge of this disease is limited, as well as prognostic factors for relapse if localized disease or response in the metastatic setting. Methods: From our database form different Spanish Hospitals, we identified a series of 89 chRCC with a localized stage and 3 patients stage IV at first diagnoses. We performed an in-depth characterization of mTOR pathway alterations, through targeted NGS and immunohistochemistry (IHC) of phospho-S6, tuberin and PTEN, and determined their impact on metastasis development and overall survival. Mutations in mitochondria and telomere maintenance genes were also assessed. TCGA kidney chromophobe project (KICH, n=64) was used for validation. Results:TP53, mTOR pathway (MTOR, TSC2 or TSC1), telomere-related genes (ATRX, TERT promoter or DAXX) and respiratory chain complex I, were mutated in 28%, 16%, 15% (26, 14, 12 of 87) and 15% (14 of 73) of primary tumors. PTEN and FLCN were mutated in four and three patients, respectively, two with bilateral tumors. IHC of phospho-S6 revealed positive staining in 37% of primary tumors (21 of 57), in association with MTOR, TSC2 and TSC1 mutations (P=0.009). Negative PTEN staining in 82% of cases (46 of 56) suggested PTEN loss as a chRCC characteristic, and was mutually exclusive with MTOR, TSC2 or TSC1 mutations (P=0.001). Weak or negative tuberin staining correlated with TSC2 mutations (P=0.02). Regarding metastasis development, TP53 mutations were enriched in malignant tumors (P=0.018), while telomere-related mutations showed a trend in the same direction. mTOR pathway mutations were associated with worse outcome. Overall survival in multivariable analysis adjusting for tumor stage gave a Hazard Ratio of 6.5 (P=0.009) This association was confirmed in TCGA-KICH (HR=11.9, P=0.05). Conclusions: Our study provides new genomic knowledge of chRCC and identifies novel markers of poor survival. Furthermore, we identified patients with mutations in mTOR pathway genes that showed high sensitivity to mTOR inhibitors.