OBJECTIVES: Although Staphylococcus aureus and Group B streptococcus (GBS) are major causes of neonatal sepsis in sub-Saharan Africa, it is unclear how these bacteria are transmitted to the neonate. METHODS: In a cohort of 377 Gambian women and their newborns, nasopharyngeal swabs were collected at delivery (day 0), and 3, 6, 14 and 28 days later. Breast milk samples and vaginal swabs were collected from the mother. Staphylococcus aureus and GBS were isolated using conventional microbiological methods. RESULTS: Most women were carriers of S. aureus (264 out of 361 with all samples collected, 73.1%) at some point during follow up and many were carriers of GBS (114 out of 361, 31.6%). Carriage of S. aureus was common in all three maternal sites and GBS was common in the vaginal tract and breast milk. Among newborns, carriage of S. aureus peaked at day 6 (238 out of 377, 63.1%) and GBS at day 3 (39 out of 377, 10.3%). Neonatal carriage of S. aureus at day 6 was associated with maternal carriage in the breast milk adjusted OR 2.54; 95% CI 1.45-4.45, vaginal tract (aOR 2.55; 95% CI 1.32-4.92) and nasopharynx (aOR 2.49; 95% CI 1.56-3.97). Neonatal carriage of GBS at day 6 was associated with maternal carriage in the breast milk (aOR 3.75; 95% CI 1.32-10.65) and vaginal tract (aOR 3.42; 95% CI 1.27-9.22). CONCLUSIONS: Maternal colonization with S. aureus or GBS is a risk factor for bacterial colonization in newborns.