This study was performed to determine the rates of breastfeeding among singletons, twins and triplets in Japan, and identify factors associated with the decision to breastfeed or bottle-feed. We analyzed a database of medical check-up of infants aged 3 to 6 months between April 2001 and July 2004 in Nishinomiya City in Japan. This medical check-up is given to almost 100% of infants in Japan and the data of 15,262 infants were analyzed. Among these, 14,963 (98.0%) were singletons, 290 (1.9%) were twins and 9 (0.1%) were triplets. Exclusive breast-feeding was chosen by 6680 (43.8%) mothers, mixed-feeding by 4645 (30.4%) mothers, and bottle-feeding with formula milk only by 3900 (25.6%) mothers. The rate of exclusive breastfeeding among twins or triplets was significantly lower than among singleton babies: 4.1% among twins or triplets, and 44.7% among singletons. Moreover, twins and triplets were independently associated with a higher rate of bottle-feeding: the odds ratio indicated that mothers who had twins or triplets were 2.44 times more likely to choose bottle-feeding with formula milk only than those who had singletons. Sucking ability at birth was associated with a higher rate of bottle-feeding: the odds ratio indicated that mothers who had infants with poor sucking ability at birth were 1.56 times more likely to choose bottle-feeding as those who had infants with normal sucking ability.