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Maternal breast milk, which is a complete food for the infant's growth, development, and health, contains fats and lipids making it susceptible to accumulation of lipophilic compounds like polycyclic aromatic hydrocarbons (PAHs). This study aimed at analyzing correlates of measured levels of PAHs in breast milk of nursing mothers to frequently used household fuels and cooking methods in Uganda, and estimate the potential health risks of PAHs to infants through breastfeeding. Sixty breast milk samples were collected from healthy and non-smoking mothers who had lived in Kampala capital city (urban area) and Nakaseke district (rural area) for at least five years. Sample extracts were analyzed for PAHs using a gas chromatograph coupled with a triple quadrupole mass spectrometer. ∑13PAHs in samples from Kampala ranged from 3.44 to 696 ng/g lw while those from Nakaseke ranged from 0.84 to 87.9 ng/g lw. PAHs with 2–3 rings were more abundant in the samples than PAHs with 4–6 rings. At least 33 % of the variance in the levels of ∑13PAHs in the breast milk samples was attributable to the fuel type and cooking methods used. Nursing mothers who used charcoal for cooking accumulated higher levels of ∑13PAHs in their breast milk samples compared to those who used firewood. Levels of ∑13PAHs in breast milk of mothers increased depending on the cooking methods used in the order; boiling< grilling< deep-frying. In all samples, hazard quotients for PAHs were −6 and 10−4, indicating that the health risks to infants due to the ingestion of PAHs in breast milk was tolerable. Further studies with large datasets on PAHs and their derivatives and, larger samples sizes are needed to confirm these findings.