Histone variants (e.g. H3) play an important role in chromatin structure and gene expression regulation of normal cells. Aims of this study were to: (1) estimate H3 and H3.3 histone mRNA expressions and their ratio in oral squamous cell carcinoma (OSCC) and oral leukoplakia (OL); (2) investigate whether H3 and H3.3 variants could play a role in the pathogenesis of OSCC and OL, also conditionally to HPV infection, age, gender, and main habits (tobacco smoking and alcohol drinking) in human beings studied. Twenty-three cases of OSCC and 20 cases of OL were examined in lesion site (LS) and juxtaposed clinically undamaged site (JUS) by RT-PCR for H3 and H3.3 histone mRNA; 13 healthy oral mucosa samples (HS) were investigated in a single site as controls. HPV DNA presence was investigated in the respective exfoliated oral mucosa cells by nested PCR (nPCR: MY09-MY11/GP5-GP6). The data showed that both H3 and H3.3 histone mRNA crude concentrations are higher in OSCC (LS=2901 ± 459 ng of H3; JUS=2699 ± 658 ng of H3; LS=3190 ± 411 ng of H3.3; JUS=2596 ± 755 ng of H3.3) than those in OL (LS=2095 ± 349 ng of H3; JUS=2192 ± 897 ng of H3; LS=2076 ± 911 ng of H3.3; JUS=1880 ± 654 ng of H3.3) and in HS (2579 ± 959 ng of H3; 2300 ± 758 ng of H3.3), although not reaching any statistical significance. Interestingly, ratio of H3/H3.3 mRNA amounts decrease both in OSCC (0.99) and OL (1.009) vs HS (1.121). No association was found for H3 and H3.3 histone mRNA expressions in OSCC and OL with respect to HPV infection and the social-demographical variables considered (P > 0.2). The overall higher expression of H3.3 in damaged tissues up to the ratio inversion in OSCC especially in HPV+ alcohol drinkers (60.0%) represents the most interesting finding, in consideration of the proven ability of alcohol to act as permeability enhancer of human oral mucosa, to alter the mucosal structure and by this dynamics could favour the penetration through the epithelial layers of HPV.