The roles of mitochondrial DNA alterations in acute appendicitis (AA) remain unclear. We evaluated the alterations of mtDNA copy number and mtDNA integrity [proportion of mtDNA templates without 8-hydroxyl-2'-deoxyguanosine (8-OHdG)] of the resected cecum appendixes in clinically suspected acute appendicitis (CSAA). A total of 228 CSAA patients, including 50 harbored negative AA (NAA), 155 true AA (TAA) without rupture and 23 TAA with rupture, who underwent appendectomies were enrolled. Tissues of resected cecum appendixes from the paraffin-embedded pathological blocks were subjected to DNA extraction, and their mtDNA copy number and mtDNA integrity were determined by quantitative real-time polymerase chain reaction (Q-PCR). During the progression of disease severity from NAA to TAA without rupture and further TAA with rupture, increases of white blood cell (WBC) counts (p=0.001), positive bacterial culture rates in turbid ascites (p=0.016) and area (p<0.001)/or volume (p<0.001) indices of resected cecum appendixes were noted among CSAA patients. On the contrary, decrease of mtDNA copy number (p=0.003) was observed during disease progression of CSAA patients, especially in female patients (p=0.007). Furthermore, lower mtDNA copy numbers were correlated with higher WBC counts (p=0.001) and larger area (p=0.003) or volume (p<0.001) indices of the resected cecum appendixes. However, such an alteration was not observed in mtDNA integrity of resected cecum appendixes. We conclude that a low mtDNA copy number of the resected cecum appendix may reflect high severity of acute appendicitis.