Background: Ovarian cancer (OC) is one of the most common cancers among women in the world. This study aimed to compare the results of endometrial and endocervical cytology with the ultimate outcome of the uterus, ovary, and fallopian tube (derived from hysterectomy or salpingo-oophorectomy) in diagnosing endometrial hyperplasia, endometrial, and OC. Materials and Methods: This cross-sectional study was conducted on 30 women with endometrial hyperplasia, 90 cases of endometrial cancer, 30 cases of OC, and 30 normal controls undergoing hysterectomy or salpingo-oophorectomy referring to Al-Zahra and Shahid Beheshti Hospitals in 2015–2017. Their basic and clinical characteristics were recorded, and then, endometrial cytology was performed by a specialist and sent to a pathological center. Results: Diagnostic value of cytology showed that out of 90 individuals with endometrial cancer, 78 (86.7%) ones were positive and 12 (13.3%) were negative with sensitivity and specificity of 86.67% and 100%, respectively. Its positive predictive values (PPVs) and negative predictive values (NPVs) were 100% and 71.4% (AUC = 0.933; P < 0.0001). In diagnosing endometrial hyperplasia out of 30 individuals with endometrial hyperplasia, there were 24 (80.0%) positive and 6 (20.0%) negative with sensitivity and specificity of 80.00% and 100%, respectively. Its PPVs and NPVs were 100% and 83.3%, respectively (AUC = 0.9000; P < 0.0001). In diagnosing, OC cytology could not detect any one of the 30 individuals with OC, with sensitivity and specificity of 0% and 100.0%, respectively. Its PPVs and NPVs were 0% and 50%, respectively (AUC = 0.500; P = 1.00). Conclusion: Cytology has a good diagnostic value for detecting endometrial hyperplasia and endometrial cancer compared to pathology; however, due to very low sensitivity in detection of OC, it could not be considered as a good diagnostic tool.