The calcifying odontogenic cyst (COC) presents with diverse histological features; thus, several subclassifications have been proposed. To evaluate the significance of the various histological features and subtypes of COC from the perspective of proliferative activity, the proliferating cell nuclear antigen (PCNA) labeling index (LI; the percentage of positive nuclei) was assessed immunohistochemically in 25 cases of COC (21 benign and four malignant). All of the benign cases were of the cystic variety and further subclassified into non-proliferative subtype (NPS; four cases); proliferative subtype (PS; eight cases); and COC associated with odontoma (COCaO, nine cases). The PCNA LI of the malignant COC (65.2 ± 5.6) was significantly higher than that of the benign COC (11.6 ± 9.0; P = 0.002). Non-proliferative subtype (6.8 ± 2.8) showed the lowest PCNA LI and PS (17.2 ± 11.2) the highest of among the three subtypes of benign cystic COC (P = 0.028). In nine cases of COCaO, six showed epithelial lining of the non-proliferative type as NPS and the other three had lining with proliferative features as PS. The PCNA LI of the latter COCaO group (14.3 ± 6.6) was significantly higher than that of the former (6.1 ± 4.3; P = 0.05), as seen between PS and NPS. These results demonstrate that PCNA LI is a possible parameter for differentiating malignant COC from benign COC and, whatever the subtypes, the proliferative features in the lining are the main factor influencing the proliferating activity of COC.