Background: In China, various assays for human papillomavirus (HPV) genotyping are currently used for cervical cancer screening. However, a proficiency test system is not available for standardizing and evaluating assay performance. The aim of this study was to evaluate the performance of clinical laboratories for their ability to discriminate 9 HPV types with the proficiency panel. Methods: The panel of 24 samples included cloned genomic DNAs for HPV types 6, 11, 16, 18, 31, 33, 39, 51 and 52 at different concentrations, which were distributed to 76 clinical laboratories. Results reported by participants were compared with the reference results. Results: The samples containing 106 IU HPV-16/ml and 106 IU HPV-18/ml were (98.7 and 96.0%, respectively) identified correctly most often. For other high-risk HPV types, about 90% of data sets correctly identified samples containing 106 GE/ml of HPV-6, HPV-31, HPV-33 and HPV-52, while HPV-51, HPV-11 and HPV-39 in 106 GE/ml were correctly identified by only 42.7, 55.6 and 21.3% of laboratories, respectively. Conclusion: Our proficiency test system provided a traceable panel and showed that the differences in performance between laboratories were high, indicating that it is necessary for the laboratories to improve their operation and standardization of HPV genotyping.