To study the relationship between the biological and morphological characteristics of oral intraepithelial neoplasms (OINs), we examined the localization of desmosome-related proteins. Twenty-seven cases of OIN3 were tentatively classified as basaloid (14 cases) or differentiated (13 cases), and the latter were further subdivided into verrucous (five cases) and acanthotic (eight cases) subtypes. All samples were stained using antibodies against desmoglein 1 (DSG1), desmocollin 3 (DSC3), junction plakoglobin (JUP) and serine peptidase inhibitor Kazal type 5 (SPINK5) domain. All variants of OIN3 showed significantly high rates of positivity for DSG1 in the basal layer (basaloid 57%; differentiated 85%), DSC3 in the surface layer (basaloid 93%; differentiated 77%) and JUP in the basal and parabasal layers (basaloid 93%; differentiated 62%). Interestingly, even the basaloid type showed areas of alternating DSG1 positivity and negativity, reflecting keratinocyte maturation. Therefore, most cases of OIN appear to have the characteristics of well differentiated squamous epithelium.