To study the epidemic status of human immunodeficiency virus type 1 (HIV-1) subtypes and sequence variation in Henan thus to explore the characteristics and sources of transmission.HIV-1 env and gag gene were amplified by nested PCR from uncultured peripheral blood mononuclear cells (PBMCs) obtained from 1287 HIV-1 carriers confirmed in Henan from 2006 to 2007. 1287 env and gag genes were obtained from the patients.Among 1287 samples, there were 4 HIV-1 strains including subtype B', C and recombinant subtype BC and AE, accounting for 95.882% (1234/ 1287), 0.466% (6/1287), 2.875% (37/1287), 0.777% (10/1287) respectively. In comparison with the sequence of the international strains of RL42, C.95in21068, 07-BC.CN.97.C54A, 01AE.TH.90.CM240, the genetic divergence was 9.327% +/- 0.245%, 5.214% +/- 0.183%, 6.278% +/- 0.194% and 5.332% +/- 0.158%, respectively.There were 4 HIV-1 strains including subtype B', C and recombinant subtype BC and AE in Henan with main dominant subtype as subtype B' which was closely related to HIV-1 strains of Thailand B'. The major transmit route in subtype B' was through blood donation in the past years while with BC, it was through sexual transmission. The major transmit routes in subtype AE were sexual transmission and blood donation. The major route of transmission in subtype C was through sexual contact.