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To identify factors affecting HIV-1 breastfeeding transmission.Longitudinal observational cohort study.HIV-1 seropositive pregnant women and seronegative controls were enrolled at a maternity hospital in Nairobi. Women and their children were followed from birth, and data on HIV-1 transmission, breastfeading, clinical illness, and growth were collected. Specimens for HIV-1 serology and/or polymerase chain reaction were obtained at birth, 2, 6, and 14 weeks, 6, 9, 12, and 18 months, and every 6 months thereafter. Children were classified as HIV-1 uninfected, perinatally, or postnatally infected. Potentially breastfeeding transmission related risk factors were compared between postnatally infected and uninfected children.Among children born to seropositive or seroconverting mothers, 317 were uninfected, 51 infected perinatally and 42 infected postnatally. Identified risk factors for postnatal transmission were maternal nipple lesions (OR = 2.3, CI 95% 1.1–5.0), mastitis (OR = 2.7, CI 95% 1.1–6.7), maternal CD4 cell count < 400 mm3 (OR = 4.4, CI 95% 1.9–9.9), maternal seroconversion while breastfeeding (OR = 6.0, CI 95% 1.8–19.8), infant oral thrush at < 6 months of age (OR = 2.8, CI 95% 1.3–6.2) and breastfeeding longer than 15 months (OR = 2.4, CI 95% 1.2–5.1). All factors, except maternal seroconversion due to its rarity, were independently associated with an increased postnatal transmission risk by multivariate logistic regression analysis.In addition perinatal antiretroviral therapies, public health strategies should address: (i) prevention of maternal nipple lesions, mastitis and infant thrush; (ii) reduction of breastfeeding duration by all HIV-1-infected mothers; (iii) absolute avoidance of breastfeeding by those at high risk, and (iv) prevention of HIV-1 transmission to breastfeeding mothers.