Clear cell renal cell carcinoma (ccRCC) is the most common renal malignancy. However, the combined clinical and biological scores commonly used to predict the clinical outcome are imperfect and need improvement. The main goal of our study was to assess the effect of mtDNA genetics on the prognosis of ccRCC patients and to explore morphologic correlation. Mitochondrial DNA copy number (mtDNAcn) variation between tumor and paired matched healthy kidney tissue was assessed by real-time quantitative PCR and expressed as a ratio in 105 patients. According to this median ratio, the cohort was divided into two groups: "LOW" (n = 53) and "HIGH" (n = 52). Cancer-Specific Survival (CSS) and Disease-Free Survival were assessed in each group. The tumor samples were classified into two subtypes (Clear or Eosinophilic cells) according to the cytoplasmic morphology. CSS was significantly reduced in the "HIGH" than in the "LOW" group with respective 5-year survival rates: 78.7% (CI 95: 64.8-95.5) and 95.5% (CI 95 87.1-100.0) (Hazard Ratio: 7.4 (CI 95: 1.9-29.9, ) in multivariate analysis, including pathological classification, tumor size, International Society of Urological Pathology grade, lymphovascular invasion, dedifferentiated pattern, necrosis and adjuvant therapy. Next-generation sequencing of mtDNA was performed on 14 tumors and matched healthy kidney tissue. No hotspot mutation or redundant large deletion was found. None of the variants or large deletions identified had an impact on prognosis. MtDNAcn variation in tumor relative to normal kidney appears as an independent prognostic factor in ccRCC, which was also associated with eosinophilic morphology. MtDNA content could be considered an additional prognostic factor, in combination with other predictive parameters. Furthermore, these results underline the importance of the role of mitochondria in ccRCC and the need for further functional studies to understand the pathophysiological mechanisms better and consider therapies targeting mitochondrial metabolism.