To investigate the potential role of mtDNA alterations during the onset of colorectal cancer, the occurrence of mtDNA variants in colorectal adenomatous (Tubular, Tubulovillous, and Villous) polyps, were studied. High resolution endonucleases and PCR-based sequence were applied to examine mtDNA variants in the ND and ATPase genes of 64 primary tissues of colorectal adeno-polyps and their matched normal controls. Forty-two variants were observed and 57% (24/42) were not previously reported in the MITODAT reference. Fifty-eight percent of these variants were germline and homoplasmic transitions. The distribution of observed mtDNA variants includes: 31% (13/42) tubular, 52% (22/42) tubulovillous, 45% (19/42) villous, and 45% (19/42) cancer (including FAP and JVP). Notably, an unreported germline variant in the ATPase 8 gene at nucleotide position (np) G8573A was observed in tubulovillous adenomas tissues. The results suggest that some specific mtDNA variants may serve as a potential biomarker for colorectal adenomatous polyps.