Objective To study the emergence of HIV-1 drug-resistance mutations and HIV-1 subtype distribution in Shanghai. Methods 33 HIV-1 isolates from cases with HIV-1 infection/AIDS were detected by drug-resistance mutation ami genotyping assay. Results PIs(protease inhibitors) drug-resistance mutations were not found in all of 33 HIV-1 isolates. The rates of NRTIs (nucleoside reverse transcriptase inhibitors)and/or NNRTIs (non-nucleoside reverse transcriptase inhibitors)drug-resistance and transitional mutations were 70% and 20% respectively in 10 HIV-1 isolates from cases failed in HAART therapy, whereas the rates of that were 4.3% and 13% respectively in 23 HIV-1 isolates from cases untreated with HAART therapy. All the transitional mutations above mentioned were T215S. In 15 hemophilia cases transmitted with contaminated blood products, all of the HIV-1 subtypes were B (belonging to group M) and in 18 intravenous drug users and sexual transmission cases , the HIV-1 subtypes were B(38. 9%),CRP01-AE(33.4%)and others including C、D、G、K and CRF02-AG. Conclusion High HIV-1 drug resistance mutation rates were found in cases which failed in HAART therapy and incomplete inhibition of replication in this area. In addition to the main subtypes B and CRP01-AE, some uncommon HIV-1 subtypes including C、D、G、K and CRF02-AG were also detected in Shanghai in China.