Objective: To evaluate the diagnostic efficiency of oral mucosa disease, especially oral squamous cell carcinoma (OSCC) and oral potential malignant disorders (OPMDs) by DNA cytometry compared with histopathological diagnosis, so as to find a convenient, simple and low-invasive method for screening and follow-up. Methods: 203 subjects with OSCC, OPMDs and other oral mucosa disease without dysplasia according to the inclusion criteria and exclusion criteria were recruited from Peking University School and Hospital of Stomatology. The mean age was (52.44±13.55) years, 98 males and 105 females. Brush biopsy was taken before scalpel biopsy at the same site. The brush biopsy sample was screened by moticytometer system for DNA cytometry after Feulgen stain, and histopathological examination were taken for the scalpel tissue. Data from DNA cytometry were used to calculate the parameters, such as sensitivity, specificity, positive and negative predictive values, odds ratios, Youden index (YI), positive and negative likelihood ratios, compared with the golden standard, histopathological diagnosis. DNA cytometry and histopathological diagnosis were performed back to back. Results: Totally, 42 OSCC and 4 tumor in situ (TIS), 39 oral leukoplakia (OLK) with dysplasia (17 mild dysplasia, 13 medium dysplasia and 9 severe dysplasia), 29 OLK with hyperplasia, 1 verrucous OLK, 83 oral lichen planus (OLP) and 5 inflammation were included in our research. We grouped the OSCC, TIS and dysplasia as the positive group and others without dysplasia as the negative group, the sensitivity of DNA cytometry was 79.07%, the specificity was 81.20%, and the diagnostic accuracy was 80.30%,We grouped the OSCC and TIS as the tumor group, OLP, OLK with hyperplasia and inflammation as the non-tumor group, The sensitivity of DNA cytometry in diagnosing OSCC and TIS was 95.65%, and the specificity was 81.2%, The diagnostic accuracy was 85.28%. positive predictive values 66.67%, negative predictive values 97.94%, ratio odds 95, positive likelihood ratio 5.09, negative likelihood ratio 0.05, and Youden index 0.77. For the dysplasia, we grouped the different dysplasia together as the dyaplasia group, OLP, OLK with hyperplasia and inflammation as the non-tumor group, the sensitivity of DNA cytometry in diagnosing dyaplasia is 60%, the specificity is 81.2%. The diagnostic accuracy is 75.8%, positive predictive values 52.17%, negative predictive values 85.59%, ratio odds 6.48,positive likelihood ratio 3.19, negative likelihood ratio 0.49, and Youden index 0.41. Conclusion: DNA cytometry is convenient and low-invasive, which can be used as an adjuvant method for screening the early OSCC and OPMDs, monitoring the prognosis of OSCC after surgery. Further large-scale and long period prospective studies are necessary to validate the better value of DNA cytometry.