The objectives of this study were to estimate the risk of vertical HIV transmission and assess the associated factors and missed opportunities for prevention in a cohort of HIV+ pregnant women (1995-2001) treated in Goiânia, Goiás, Brazil, with follow-up of their children until 2005. Three data sources were compared: Information System on Reportable Diseases (SINAN), Information System on HIV+ Pregnant Women and Exposed Children (SISGHIV), and patient clinical charts. The study estimated the vertical transmission rates, factors associated with vertical transmission, and use of antiretroviral therapy. 276 HIV+ women were identified (322 pregnancies), and there were 70 HIV+ children. Overall risk of vertical HIV transmission was 27.8%. The vertical transmission rate was 40.8% in the group without prophylaxis and 1% in the group with adequate prophylaxis, i.e., a 97.5% reduction in transmission risk. Year of delivery, consultation with a specialist, and no history of injecting drug use were factors associated with adequate use of antiretroviral therapy. The study showed an important reduction in the risk of vertical transmission in pregnant women who received adequate therapy, besides identifying missed opportunities for prevention.