Vertical HIV transmission rates and associated factors among mother-infant pairs cared for at a Brazilian reference centre from 1988 to 1993 (period 1), and from 1996 to 1999 (period 2) were evaluated. A total of 150 and 239 infants born to HIV+ mothers were enrolled at birth during these periods. No zidovudine prophylaxis was available in period 1. In period 2, 92.4% of the infants were exposed to zidovudine (54% started at delivery or in the post-natal period). During period 1, 25 of 129 infants were found to be infected (19.4%; 95% confidence interval [CI]=13-27) vs 20 of 232 (8.6%; 95% CI=5-13) during period 2 (P <0.01). After controlling for co-variables, this decline was due to zidovudine prophylaxis, either with complete (odds ratio [OR]=0.24; 95% CI=0.08-0.70) or incomplete (OR=0.37; 95% CI=0.17-0.81) regimens. Premature rupture of membranes (OR =3.2) and rhesus-negative blood type of the infant (OR=2.6) facilitated transmission. Although confirming the protective effect of zidovudine prophylaxis, alternative approaches aimed at pregnant women identified late are needed for this population.