Background Several methods have been applied to detect death cells in tissue, cell culture, and fluid samples. We aimed to compare the cytological and immunocytochemical methods for detecting apoptotic cells in cervicovaginal smears. Methods Cervicovaginal smears were taken from 102 women for various gynecological complaints. The slides were stained using the Papanicolaou (Pap)-staining method for cytological evaluation. Cleaved caspase 3 (CC3) antibody was used to detect apoptosis by immunocytochemically, and H-Score was used for the evaluation. In Pap-stained smears, apoptosis was detected and evaluated using our new scoring system by the examination of morphological changes of epithelial cells such as apoptotic bodies, blebbing, karyopyknosis, karyorrhexis, and karyolysis. We used Kappa analysis to understand whether there is an agreement between cytological and immunocytochemical methods for detecting apoptotic cells. Results Cytological and immunocytochemical methods showed similarities at a moderate level (kappa = 0.482, P < .001). The cytological and immunocytochemical scores were also similar to each other at a fair level (kappa = 0.373, P < .001). Pap smears had a sensitivity of 64.40% (95% CI: 50.12-76.01), specificity of 86.04% (95% CI: 72.65-94.83), positive likelihood ratio of 4.62, negative likelihood ratio of 0.41, positive predictive value of 86.36%, negative predictive value of 63.79%, and overall probability of 73.53% compared to immunocytochemical staining. Conclusions Our results demonstrate that Pap smear and cytological scores alone were not good enough to identify apoptosis compared to the immunocytochemical studies. However, because of its high specificity, it may still be an adequate method to detect apoptotic cells.