〔Abstract〕 Objective To investigate the expression and significance of S100 and cluster of differentiation (CD) 43 immunohistochemical staining in adenoid cystic carcinoma (ACC) and basal cell adenoma (BCA). Methods Focal specimens of 21 patients with ACC and 8 patients with BCA who were surgically removed from Zhongshan Hospital, Fudan University (Xiamen Branch) from January 2018 to December 2023 were collected. Immunohistochemical EnVision two-step staining of S100 protein and CD43 were performed and their expressions were analyzed. Results S100 protein labeling showed that no S100 protein positive spindle interstitial was found in all ACC cases (0.0 %), while S100 protein strongly positive spindle interstitial was found in BCA cases (62.5 %), the difference was statistically significant (P < 0.01). The CD43 labeling showed that the CD43 positive expression rate of ACC tumor cells was 71.4 %, while that of BCA tumor cells was 12.5 %, the difference was statistically significant (P = 0.01). Conclusion The combination of S100 and CD43 immunohistochemical staining is helpful for the differential diagnosis of ACC and BCA.