BACKGROUND: Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are the common malignant neoplasms of the skin. The p63 is a p53 homologue which is considered to be a reliable keratinocyte stem cell marker. Bcl-2 plays a key role in cell longevity by preventing apoptosis, whereas the bcl-6 gene functions as a transcriptional repressor. The p16-CDK4/6 complex arrests the cell cycle at G0 /G1 phase. In the present study, the expression of p63, bcl-2, bcl-6, and p16 in BCC and SCC was evaluated. METHODS: Forty-seven BCCs and 43 SCCs were selected and microarrayed in paraffin blocks. Immunohistochemical analysis was performed with specific antibodies for bcl-2, bcl-6, p16 and p63. RESULTS: p63 was found to be expressed in all BCCs and SCCs. Bcl-2 was exclusively expressed in BCCs (100%), but there was negative expression in SCCs, whereas bcl-6 was positively expressed in 18.2% of SCCs, and was negative in BCCs. In SCCs, p16 was expressed at high frequency (47.7%) than in BCCs (14.9%). The expression of p16 was correlated with the histologic grades of SCCs. CONCLUSION: The different patterns of bcl-2, bcl-6, p63 and p16 protein expression between BCCs and SCCs may represent the different histogenesis and morphologic features of two lesions.