To examine the relationship between measures of mother’s caretaking, practice and individual agency on acute diarrhea and respiratory tract infections (ARTIs) of Indonesian children. Using population-based household data from the Indonesian Demographic Health Surveys for 2002–2003 (n = 9,151 children) and 2007 (n = 9,714 children), we selected 28 indicators related to mother’ caretaking, and applied principal component analysis to derive indices for access to care, practice and experience, and agency. The association between index quartiles (level 1–4) and the prevalence of diarrhea and ARTIs in the youngest child <5 years of age was assessed with multivariate logistic regression adjusting for socioeconomic status, residence type, mother’s age and education, family size, child’s age and sex, immunization status and received vitamin A supplementation. Moderate levels (level 3) of practice and experience were associated with decreased diarrheal risk (adjusted OR 0.86, 95 % CI 0.75–0.98), but not for ARTIs. Children of mothers with higher levels (level 4) of agency were protected against both diarrhea (adjusted OR 0.68, 95 % CI 0.60–0.77) and ARTIs (adjusted OR 0.77, 95 % CI 0.66–0.91). Stratified analyses with child’s age and mother’s education, and tests of interaction, showed that agency had a stronger effect on diarrhea and ARTIs prevalence in children <2 years of age. Maternal caretaking, especially agency, is strongly associated with lower prevalence of diarrhea and ARTIs in younger children. Interventions specifically designed to promote maternal autonomy and decision-making may lead to improved child health.