We studied 1139 mother-infant pairs where the mother had had at least one vaginal swab in the month before delivery and their babies had had gastric and ear swabs taken immediately after delivery. The prevalence of vaginal carriage of Staphylococcus aureus was 5.9% among 1139 pregnant women within 1 month of delivery. The colonisation rate of S. aureus in newborns was tenfold higher when the mother was a vaginal carrier than when she was not (31.3% vs. 2.7%; relative risk 11.6 [95% CI 7.0, 19.2]; P < 0.05). Among carriers, delivery by caesarean section compared with the vaginal route, significantly decreased the likelihood of S. aureus colonisation in the newborns (15.4% vs. 41.5%; relative risk 0.35 [95% CI 0.14, 0.98]; P < 0.03). No S. aureus colonisation was detected in the mothers of 58% of the colonised newborns suggesting extra-delivery colonisation routes. Consequences for newborns were unclear as only one case of S. aureus neonatal sepsis was observed.