Objective To evaluate the clinic value of flow through hybridization and real-time PCR in detecting HPV of cervical carcinoma. Methods 190 cases of HPV of cervical carcinoma were detected by using flow through hybridization and real-time PCR, respectively. Results There were 113 positive cases (59.5%) detected with flow through hybridization, and the sensitivity, specificity, positive-predictive value and negative-predictive value in detecting HPV for cervical carcinoma were 58.1％, 39.2％, 47.8％ and 49.4％ respectively. There were 106 positive cases (55.8%) detected with real-time PCR, and the sensitivity, specificity, positive-predictive value and negative-predictive value in detecting HPV for cervical carcinoma were 54.8％, 43.3％, 48.1％and 50.0％ respectively. There was a concordance rate of 87.9% in the detection of HPV between two methods. Conclusion The results of this study suggest that there are no significant differences in the detection of HPV between flow through hybridization and real-time PCR. The detective rate may be improved in screening cervical carcinoma by combination of the two methods.