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Hepatitis C was the most popular chronic infectious liver disease worldwide. It was identified that Hepatitis C virus (HCV) infection could lead to mitochondrial dysfunction, though the mechanism was not fully understood. To investigate whether mtDNA copy number could be affected by HCV infection and be associated with clinical features of HCV patients, mtDNA copy numbers were analyzed in 242 patients with HCV infection and 226 matched control samples. The results suggested that mtDNA copy numbers significantly decreased in HCV patients (68.80 ± 3.33) than in control samples (81.54 ± 4.50) (p = 0.022). When males/females were separated from total patients to compare mtDNA copy numbers with gender matched controls, mtDNA copy numbers still significantly decreased in male HCV patients (p = 0.002). Further analysis indicated that level of high-density lipoprotein cholesterol (HDL-C) was negatively correlated with mtDNA copy numbers in total HCV patients (r = −0.128,p = 0.047), and this correlation was more significant in male HCV patients (r = −0.266,p = 0.030). Intriguingly, aspartate amino-transferase (AST) showed positive correlation with mtDNA copy numbers (r = 0.260,p = 0.034) in male HCV patients. Our results indicated that mtDNA copy numbers depleted and correlated with clinical features in male HCV patients. [ABSTRACT FROM AUTHOR]