Objective To provide a better pathological method for clinical diagnosis of endometrial lesions. Design Comparing the accuracy of hematoxylin-eosin (H-E) with Papanicolaou stain for endometrial cytology. Setting The First Affiliated Hospital of Xi’an Jiaotong University. Population or Sample 180 patients. Methods Endometrial slides were stained by H-E and Papanicolaou methods, respectively. The cytology between them were compared, with histology as standard control, as well as the cost performance. Main Outcome Measures The dyeing degree of satisfaction, sensitivity, specificity, Cohen’s kappa coefficient, false positive rate, false negative rate, positive likelihood ratio, negative likelihood ratio, Youden index, positive predictive values, and negative predictive values. The price and service time of dye, dyeing efficiency, and dyeing time. Results The sensitivity of H-E stain was higher than that of Papanicolaou stain. The specificity of H-E stain was same to that of Papanicolaou stain. Cohen’s kappa coefficient indicatied a high consistency between them. The morphological characterization of Papanicolaou stain were superior to those of H-E stain. The cost performance of H-E stain was lower. Conclusions In terms of overall evaluations and economic benefits, H-E stain is better than Papanicolaou stain. If a small sample volume of endometrial cells, Papanicolaou stain is recommended. Funding The Clinical Research Award of the First Affiliated Hospital of Xi’an Jiaotong University, China, the Major Basic Research Project of Natural Science of Shaanxi Provincial Science and Technology Department, the Key Research and Development Project of Shaanxi Provincial Science and Technology Department. Keywords: H-E stain, Papanicolaou stain, Endometrium, Cytology