As in most countries, the epidemiology of HIV/AIDS in Vietnam consists of many noncontiguous epidemics of varying magnitudes involving groups separated by time, geography and risk-taking behaviors. To better understand the dissemination patterns of HIV infection in Northern and Southern Vietnam, we conducted a cross-sectional study of plasma samples collected from 118 HIV-infected injection drug users (IDU; 41 from the North and 77 from the South) and 45 commercial sex workers (CSW; from the South) during the five-year period, 1995 to 1999. A 293-bp region, spanning the principal neutralizing domain (V3 loop) of the gp120-encoding HIV env gene, was amplified from RNA extracted from individuals in the North (Hanoi, Hai Phong, Lang Son and Quang Ninh in the north) and the South (Ho Chi Minh City, An Giang, Can Tho, Khanh Hoa, Kien Giang, Nha Trang, and Da Nang). Of interest were particular "signature sequences" which were geographic specific and showed similarity to sequences found in neighboring countries. For example, the high prevalence of a methionine substitution near the peak of the V3 loop and a methionine substitution plus asparagine deletion in the C3 region among IDU in the North suggested independent introduction of HIV subtype E in the North and the South. Moreover, the low nucleotide sequence diversity and high prevalence of valine substitution among IDU in Northern Vietnam suggest cross-border transmission of HIV, particularly from China to Northern Vietnam (Table 1).