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Background The histopathological diagnosis of oral premalignant lesions (OPLs) such as oral epithelial dysplasia (ED) and carcinoma in situ (CIS), as well as epithelial hyperplasia (EHP), is important for the early detection and precise treatment of oral squamous cell carcinoma. However, the standardization of detection and treatment by histological criteria alone remains challenging owing to the complicated and varied histology. We evaluated practically useful immunohistochemical (IHC) markers that might complement the histopathological diagnosis of OPLs. Methods We re-evaluated the histopathological diagnoses and IHC patterns of Ki-67, TP53, CK13, and CK17 in 200 cases of OPLs and performed multiple logistic regression analyses for their predictive accuracy. Results We identified and compared atypical IHC patterns in OPLs and in the normal epithelium. Ki-67 expression showed specific patterns in categorized OPLs as EHP, low-grade dysplasia (LED), high-grade dysplasia (HED), and CIS. Multiple logistic regression analyses in the quadrant categories revealed that EHP and CIS had high predictive accuracies of 90.1% and 96.2%, respectively, and in binary categories, combined EHP and LED versus combined HED and CIS showed predictive accuracies of 92.1% and 89.9%, respectively. Binominal logistic regression analysis between each quadrant category revealed satisfactory predictive accuracy of EHP vs. LED, LED vs. HED, and HED vs. CIS (75.2%, 78.9%, and 87.9%, respectively), and Ki-67 showed the highest adjusted odds ratio, followed by TP53. Conclusion The proposed atypical IHC patterns might serve as useful markers to supplement the morphological diagnosis of OPLs, and established IHC methods for Ki-67 and TP53 might provide stable results.