Perinuclear anti-neutrophil cytoplasmic antibody (pANCA) is a serological marker associated with various immune-mediated diseases whose clinical significance and possible diagnostic roles in ulcerative colitis (UC) are still unclear. We aimed to evaluate the prevalence of pANCA expression and its association with clinical findings and disease course in Korean patients with UC. This study included 484 patients with UC who were diagnosed and treated between 1990 and 2006 at Severance Hospital, Yonsei University, Seoul, Korea, and were followed for at least 1 year. Clinical findings at diagnosis, disease extent, treatment modalities used, and cumulative relapse rates were analyzed and compared to pANCA expression. Of the 484 patients, 405 (83.7%) were evaluated for pANCA and were eligible for analysis. The overall pANCA prevalence was 22.1%, with a female preponderance (male, 21.5%; female, 31.6%; P < 0.05). Proctitis was more common in pANCA-negative patients (pANCA-negative, 37.6%; pANCA-positive, 25.2%, P < 0.05). UC activity index and cumulative relapse rates were higher in pANCA-positive patients. However, there were no significant differences in the cumulative probability of steroid and immunosuppressant use and operation rate between the two groups. The prevalence of pANCA expression in Korean patients with UC was relatively low compared to that in Western countries. Although UC patients with pANCA expression had more severe clinical findings at diagnosis and higher cumulative relapse rates in our study, further prospective studies are warranted to clarify whether pANCA positivity influences the initial clinical presentation or disease aggressiveness.