Vertical transmission of HIV-1 is caused by multifactorial factors. To access the relationship of viral factors involving in perinatal transmission of HIV-1 subtype E, which is the predominant type in Thailand, plasma viral load, blood CD4+ lymphocyte level, heteroduplex mobility, and V3 sequence of the HIV-1 envelope gene were studied in 32 transmitting and 25 non-transmitting mothers. We found that HIV-1 subtype E vertical transmission was strongly associated with high maternal plasma viral RNA (> 4 x 10(4) copies/ml) and high genetic diversity of envelope gene determined by heteroduplex mobility (< 0.9). The variation of nucleotide sequences in envelope gene of subtype E vertical transmission could not determine in V3 region. Hence, plasma viral load and heteroduplex mobility can be used as prediction factors in vertical transmission of HIV-1 subtype E.