To investigate whether previously described sex differences in virological and immunological markers in vertically infected children are preceded by sex differences in the overall risk or timing of mother-to-child transmission (MTCT) we analysed 3231 mother-child pairs enrolled in the European Collaborative Study. Girls were at a 1.5 times increased risk of MTCT overall, but the sex effect was limited to elective caesarean section deliveries, suggesting that girls may have an increased risk of intrauterine transmission compared with boys.