Change of mitochondrial DNA (mtDNA) copy numbers is considered to be an important hallmark of cancers. However, whether quantitative changes in mtDNA occur during the initiation and progression of colorectal cancer remains to be determined. Quantitative change in mtDNA was observed during the initiation and progression of colorectal cancer and possible correlations of the mtDNA copy number in colorectal cancer with the clinicopathological stage were investigated. Tumor tissues and the corresponding non-cancerous tissues were surgically resected from 24 colon and 20 rectal patients between 2008 and 2009. β-actin expression was quantified in all of the specimens, and the copy numbers were calculated. In colorectal cancer, the quantitative changes of mtDNA exhibited a significant increase. In 24 cases of colon cancer, the average relative mtDNA copy number ratios were 115.15±31.57 in cancer tissues and 54.09±13.22 in the corresponding non-cancerous tissues (p<0.01). Furthermore, in 20 cases of rectal cancer, the ratios were 145.6±43.83 in cancer tissues and 55.58±12.47 in the corresponding non-cancerous tissues (p<0.001). Following correlation with clinicopathological data, change of the mtDNA copy number in colorectal cancer exhibited a significant association with clinicopathological stage, but no association with gender. Moreover, this increase was particularly marked in stages Ⅰ and Ⅱ. Our results indicate that mtDNA copy number plays a significant role during the initiation and progression of colorectal cancer, particularly during early clinicopathological stages.