Ulcerative colitis (UC) is an inflammatory bowel disorder characterized by continuous colonic mucosal inflammation that extends proximally from the rectum. The pathogenic mechanisms underlying UC remain unknown. Free-radical-elicited oxidative damage to macromolecules has been established as a contributory factor in UC. It is well known that the mitochondrial genome is more susceptible to increased oxidative damage than nuclear DNA. One of the best-described mtDNA mutations is the ΔmtDNA4977 (mtDNA 4977 bp) or common deletion. The aim of this study was to investigate the relationship between ΔmtDNA4977 and UC. We studied the ΔmtDNA4977 150 patients with UC (64 men, 86 women; mean age, 36.7 ± 11.6 years) and 250 disease-free controls (137 men, 113 women; mean age, 35 ± 12.1 years) in northern Iran. After DNA extraction from colon biopsies, gap polymerase chain reaction (Gap-PCR) was performed. The frequency of ΔmtDNA4977 was significantly different between the UC patients and the control group (78.7% vs. 16.8%, P<0.001). We found that ΔmtDNA4977 was more likely to be present in the patients of younger age (≤ 50 years, P=0.021). The mtDNA deletion was also significantly associated with the increased risk of an extensive form of colitis. Our study indicates that the ΔmtDNA4977 may play a role in the pathogenesis of UC. However, the findings need to be verified in large population-based prospective studies for more rigorous analyses of subgroups.