OBJECTIVE The aim of this study was to demonstrate that the presence of atypical perinuclear antineutrophil cytoplasmic antibodies (pANCA) in indeterminate colitis (IC) patients and the potential role of pANCA for predicting the patients either with ulcerative colitis (UC) or Crohn's disease (CD) for UC and CD. METHODS Outpatients and inpatients from the hospital were retrospectively enrolled between April 2008 and December 2010. A total of 25 IC patients enrolled in the present study. Subsequently, 25 randomly selected serum samples were tested for pANCA in our laboratory. Determination of pANCA was performed by enzyme linked immunosorbent assay. RESULTS Minimum follow-up was 12 months. The mean duration of disease was 20.52 months. The diagnosis was changed to UC in 13, to CD in 5 patients. The remaining 7 patients are still classified with IC, with mean disease duration of 21.29 months. Duration of disease differs statistically when comparing pANCA positive versus pANCA negative. A positive correlation was found between IC and disease location in our study. CONCLUSIONS Patients with an initial diagnosis of IC who have positive serology are given a definitive diagnosis of UC or CD, respectively, more often than patients with negative serology.