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In 2000, Thailand implemented a national program to prevent mother-to-child HIV transmission (PMTCT).To describe the effectiveness of the prevention of mother-to-child HIV transmission program in Thailand.A register of HIV-exposed children at birth was created with follow-up of infection status. The register included children born to HIV-infected women between 1 January 2001 and 31 December 2003 at 84 public health hospitals in six provinces of Thailand. The main outcome measure was HIV infection in children.A total of 2200 children born to HIV-infected mothers were registered. Of these mother–infant pairs, 2105 (95.7%) received some antiretroviral prophylaxis, including 1358 (61.7%) who received the complete short-course zidovudine regimen during pregnancy and labor for the mother and after birth for the infant, with or without other antiretrovirals. HIV infection outcome was determined for 1667 (75.8%) children, of whom 158 [9.5%, 95% confidence interval (CI), 8.1–11.0%] were infected. Transmission risk was 6.8% (95% CI 5.2–8.9%) among 761 mother–infant pairs that received the complete zidovudine regimen alone, and 3.9% (95% CI, 2.2–6.6%) among 361 mother–infant pairs that received the complete zidovudine regimen combined with other antiretrovirals, usually nevirapine. The overall transmission risk from this cohort, including all antiretroviral prophylaxis combinations, is estimated to be 10.2%.The Thai national PMTCT program is effective in reducing mother-to-child transmission risk from the historical risk of 18.9–24.2%. The addition of nevirapine to short-course zidovudine beginning in 2004 may further improve program effectiveness in Thailand.