Purpose The true aggressive behavior of oral cavity BSCC compared to SCC has been debated, and the study of disturbances in cell cycle proteins may help understand the biological behavior in both variants. The aim of this study was to investigate the p53 and p16 status in 32 SCC and 16 BSCC of oral cavity. Methods Immunohistochemistry was used to assess these proteins' status. The association between p53 and p16 with clinicopathological features and prognostic value were evaluated. Results A high prevalence of p53 disruption was observed in both variants (84.4% of 32-SCC and 81.2% of 16-BSCC; p = 0.78). The BSCC showed a higher prevalence of high p16 expression (86.7% of 15) when compared to SCC (61.3% of 31); however, this difference did not reach statistical significance (p = 0.08). In the SCC variant, cases with high p16 expression showed a lower overall survival. Protein p53 showed association with tobacco use, but with no other clinicopathological features. Conclusions Our results suggest that p53 and p16 cell cycle disruptions are common findings in oral cavity SCC, as well as in BSCC. A higher prevalence of p16 overexpression in oral BSCC cases may be related to carcinogenesis process.