Background Inflammatory bowel disease (IBD) has been a worldwide health care challenge with a continually increasing incidence in India. Spectrum of IBD mainly includes ulcerative colitis (UC) and Crohn's disease (CD). Pharmacological and surgical treatments differ widely in CD and UC; hence, establishment of a correct diagnosis is of paramount importance as it critically influences the disease outcome. Aim The aim of this study was to assess the utility and diagnostic accuracy of immunohistochemical profile of beta-catenin and retinoblastoma protein in IBD as potential biomarkers. Study design This is a cross-sectional observational study. Material and methods Data of 61 cases of IBD with UC and CD were retrieved from the Department of Pathology. Immunohistochemical markers beta-catenin and retinoblastoma protein were applied on the paraffin blocks of these cases, and their results were interpreted. Results Of the 61 cases, 49 cases of UC showed positivity for beta-catenin with 100% sensitivity and 75% specificity and nine cases of CD showed positivity for retinoblastoma protein with 75% sensitivity and 95.92% specificity. Three cases were IBD unclassified. Overall, accuracy of beta-catenin in UC was found to be 95.08% and that of retinoblastoma protein in CD was 91.80%. Conclusion Our study provides insights into the expressions of these specific immunohistochemistry markers and their significance in the differentiation of IBD into UC and CD.