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Background: Operational effectiveness of large‐scale national programmes for the prevention of mother to child transmission (PMTCT) of HIV in sub‐Saharan Africa remains limited. We report on HIV‐free survival among nine‐ to 24‐month‐old children born to HIV‐positive mothers in the national PMTCT programme in Rwanda. Methods: We conducted a national representative household survey between February and May 2009. Participants were mothers who had attended antenatal care at least once during their most recent pregnancy, and whose children were aged nine to 24 months. A two‐stage stratified (geographic location of PMTCT site, maternal HIV status during pregnancy) cluster sampling was used to select mother‐infant pairs to be interviewed during household visits. Alive children born from HIV‐positive mothers (HIV‐exposed children) were tested for HIV according to routine HIV testing protocol. We calculated HIV‐free survival at nine to 24 months. We subsequently determined factors associated with mother to child transmission of HIV, child death and HIV‐free survival using logistic regression. Results: Out of 1448 HIV‐exposed children surveyed, 44 (3.0%) were reported dead by nine months of age. Of the 1340 children alive, 53 (4.0%) tested HIV positive. HIV‐free survival was estimated at 91.9% (95% confidence interval: 90.4‐93.3%) at nine to 24 months. Adjusting for maternal, child and health system factors, being a member of an association of people living with HIV (adjusted odds ratio: 0.7, 95% CI: 0.1‐0.995) improved by 30% HIV‐free survival among children, whereas the maternal use of a highly active antiretroviral therapy (HAART) regimen for PMTCT (aOR: 0.6, 95% CI: 0.3‐1.07) had a borderline effect. Conclusions: HIV‐free survival among HIV‐exposed children aged nine to 24 months is estimated at 91.9% in Rwanda. The national PMTCT programme could achieve greater impact on child survival by ensuring access to HAART for all HIV‐positive pregnant women in need, improving the quality of the programme in rural areas, and strengthening linkages with community‐based support systems, including associations of people living with HIV., Background Worldwide, 2.5 million children younger than 15 years were living with HIV in 2009, and more than 90% had been infected via mother to child transmission (MTCT) of HIV [...]