Mitochondria are ubiquitous organelles in eukaryotic cells, which are mainly responsible for the regulation cellular energy metabolism, generation of free radical, and the execution of apoptotic pathways. Abnormal oxidative phosphorylation and aerobic metabolism are the result of mitochondrial dysfunction and are thought to be involved in tumorigenesis. In the past decades, numerous mutations in both the coding and control regions of mitochondrial DNA (mtDNA) have been extensively examined and confirmed in a broad range of primary human cancer, underscoring that accumulation of mtDNA alterations may be a critical factor in eliciting persistent mitochondrial defects and consequently contribute to cancer initiation and progression. However, the roles of these mtDNA mutations in the carcinogenic process remain largely unknown. This review outlines a wide variety of mtDNA mutations identified in common human malignancies and highlighted recent advances in understanding the causal roles of mtDNA variations in neoplastic transformation and tumor progression. In addition, it briefly illustrates how mtDNA alterations activate mitochondriato-nucleus retrograde signaling so as to modulate the expression of relevant nuclear genes or induce epigenetic changes and promote malignant phenotypes in cancer cells. These findings strongly indicates that mtDNA mutations could be used as a diagnostic biomarker for early detection of cancer and as a potential target for the therapy of cancer, but continued investigations are definitely required to further elucidate the functional significance of specific mtDNA mutations in cancer.