Background: Worldwide, the incidence of inflammatory bowel disease (IBD) is increasing. This study aims to evaluate the diagnostic value of two serological markers, atypical perinuclear anti-neutrophil cytoplasmic antibodies (atypical-P-ANCA) and anti-Saccharomyces cerevisiae antibodies (ASCA), with the intent to determinetheir relationship to ulcerative colitis (UC) and Crohn's disease (CD), in addition to the location and extent of bowel involvement., Methods: There were 97 patients enrolled in this study, 72 diagnosed with UC and 25 with CD.The control group consisted of 40 healthy individuals. ASCA was determined by enzyme-linked immunosorbent assay (ELISA) and atypical-P-ANCA by indirect immunofluorescence assay (IIF). For data analyses, we used the chi-square and independent t-tests. Significance was considered to be p<0.05., Results: For CD, the sensitivityof ASCA was 16% and its specificity was 97%.ASCA had a specifity of 90% in UC patients. The atypical P-ANCA test had a sensitivity of 44% and specificity of 86% for UC. The positive predictive value (PPV) for atypical P-ANCA in UC patients was 78% and for the negative predictive value (NPV), it was 58%.There was no correlation between ASCA and atypical P-ANCA results and the location of gastrointestinal (GI) involvement in CD (p=0.61) and UC (p=0.28) patients., Conclusion: According to the results, ASCA and atypical P-ANCA markers are not useful for IBD screening. Our study suggests that atypical P-ANCA is a useful parameter to differentiate UC from CD. However, ASCA is of limited value for screening and differentiating UC from CD.