Craniopharyngioma (CP) is a pathologically benign tumor with high incidence of recurrence and poor prognosis. DNA ploidy, S-phase fraction (SPF), and G2 phase/mitosis phase + S phase (G2/M + S) measured by flow cytometry (FCM) have been shown to correlate with cell cycle characteristics and clinical prognosis of other tumors. By use of FCM and terminal deoxynucleotide transferase-mediated dUTP nick end labeling (TUNEL) peroxidase, we compared DNA content, SPF, G2/M + S, necrosis and apoptosis in non-recurrent and recurrent tumor cells of CP from 63 cases including 32 adamantine epitheliomas (AEs) and 31 squamous papillary tumors (SPTs), and the ultrastructure of the CP cell was observed by transmission electron microscopy. Although no obvious differences between DNA content and necrosis and apoptosis rate were observed in subgroups of CPs, SPF and G2/M + S for recurrent tumors were statistically higher than those for recurrence-free tumors, and the recurrence rate of AE tumors is higher than that of SPT. Therefore, CP cells are diploid, and SPF and G2/M + S are related to recurrence of CP.