The epithelial lining of odontogenic keratocysts exhibits either parakeratosis or orthokeratosis. In 2005, the WHO classified odontogenic keratocysts with parakeratosis as keratocystic odontogenic tumors (KCOT). Odontogenic keratocysts with orthokeratosis were not classified as odontogenic tumors, but instead referred to as orthokeratinized odontogenic cysts (OOC). To clarify the difference between these two lesions, we investigated their biological characteristics using immunohistochemical studies for cytokeratins (CK) in KCOT and OOC as well as in dentigerous cysts (DC), radicular cysts (RC) and dermoid cysts (DMC). We examined twenty-five cases of KCOT, fifteen cases each of OOC, DC and RC, and ten cases of DMC. We studied the immunohistochemical expression of CK10, 13, 17 and 19. To evaluate the immunohistochemical staining pattern, we divided the epithelial lining of the lesions into three layers (surface layer: su, spinous layer: sp, basal layer: ba). For CK10, most OOC and DMC specimens of su and sp were positive. For CK13 and 19, most KCOT, DC and RC specimens of su and sp were positive. For CK17, most KCOT specimens of su and sp were positive. The percentages of total CK expression of su and sp, and ba of CK19 differed significantly between the lesions (P < 0.001). These results support the hypothesis that OOC originate from not the odontogenic apparatus, but the oral epithelial component.