Whether or not the protective effects of breastfeeding last during or after a shift to a weaning diet is not clear. In the present study, we examined the effects of breastfeeding on hospitalization for respiratory tract infections and diarrhea in early childhood in Japan. Data were extracted from a nationwide longitudinal survey of Japanese children. We restricted the study participants to singleton children who were born after 37 gestational weeks and whose information on feeding practice during infancy were included (n = 43,367). We used logistic regression models to evaluate the associations of breastfeeding with hospitalization for the two diseases among young children (i.e., between ages 6 and 18 months, between ages 18 and 30 months, and between ages 30 and 42 months, respectively), adjusting for children's factors (sex, birth weight, childcare attendance and presence of siblings) and maternal factors (educational attainment and smoking status). Breastfeeding compared with infant formula was not associated with reduced risk of hospitalization for diarrhea during the periods we examined. Although breastfeeding was not associated with reduced risk of hospitalization for respiratory tract infections between ages 6 and 18 months, breastfeeding showed protective effects after that period: the adjusted odds ratios (95 % confidence intervals) of exclusive breastfeeding were 0.82 (0.66-1.01) between ages 18 and 30 months and 0.76 (0.58-0.99) between ages 30 and 42 months. Breastfeeding may have long-term protective effects on hospitalization for respiratory tract infections after infancy, but not for diarrhea.