Background This study was performed in order to investigate the relationship between breastfeeding and the antibody response after vaccination with conjugate vaccines against Hib and pneumococcal diseases. Methods This was an open non-randomised multi-centre study enrolling 101 healthy Swedish infants. PncCRM was administered concomitantly with DTaP/IPV/Hib at 3, 5, and 12 months at separate site. Duration of breastfeeding was calculated for days of almost exclusive as well as of total (any form of) breastfeeding. Results At 13 months of age 6 out of 83 children did not reach 0.2 μg/ml against serotype 6B, and five of these were breastfed less than 90 days (Fisher's Exact test, P = 0.011). Four children did not reach 1 μg/ml against Hib and all those were breastfed less than 90 days (Fisher's Exact test, P = 0.008). One month after the second dose, at 6 months of age, children breastfed 90 days or more showed significantly higher GMC against serotype 14 ( P = 0.003). Conclusion This study indicates that children exclusively breastfed 90 days or more might get a better serological protection against Hib, and the pneumococcal serotypes 6B and 14 after vaccination, compared to children less breastfed.