Abstract: Objective To investigate the drug resistance of human immunodeficiency virus (HIV)-1 among HIV infection cases in Shanghai and provide evidence for the improvement of anti-retrovirus (ARV) treatment. Methods A total of 1296 HIV infection cases detected in Shanghai in 2013 were surveyed by detecting their plasma samples. DNA were extracted for reverse transcription-polymerase chain reaction (RT-PCR) amplification, sequencing. subtype identification. The drug resistance results were compared with those in international HIV drug resistance database. Results A total of 1085 pol gene fragments were obtained from these cases, in which 651 belonged to CRF01_AE (60.0％), 253 belonged CRF07_BC (23.3％), 97 belonged to subtype B (8.9％), 52 belonged to CRF08_BC(4.8％), 12 belonged subtype C(1.1％), 10 belonged to CRF01_B(0.9％), 2 belonged to subtype F2 (0.2％), 2 belonged to subtype G(0.2％), 5 belonged to CRF02_AG(0.5％)and 1 belonged to CRF03_AB(0.2％). The prevalence of primary drug-resistance was 1.4％. The mutation associated drug resistant rates to nucleoside reverse transcriptase inhibitors (NRTI), non-nucleoside reverse transcriptase inhibitors (NNRTI) and integrase inhibitor (IN) were 0.3％ (3/1085),0.9% (9/1085) and 0.2％ (2/1085) respectively. One case of mutation associated drug resistance to protease inhibitors (PIs) and to NNRTIs were detected respectively. Conclusion The primary drug resistant gene mutation associated drug resistant rate was in decline in HIV infection cases in Shanghai during 2007-2013, which declined from 4.5% in 2007 to 1.1% in 2013. HIV with resistant gene CRF01_AE was predominant and mainly circulated in MSM. A very few HIV infection cases were resistant to 2 antiviral drugs. It is necessary to strengthen the surveillance for HIV with resistant gene CRF01_AE, especially in MSM.