BACKGROUND: Accumulating evidence has shown that high-quality early childhood education and care may be an effective way of promoting children's optimal health and development, especially for the most disadvantaged. However, socially disadvantaged families are less likely to enroll children in center-based childcare. In this study, we explored characteristics associated with use of center-based childcare among Japanese families. METHODS: We used data from two Japanese birth cohorts in 2001 (n = 17,019) and 2010 (n = 24,333). Enrollment in center-based childcare was assessed at the ages of three and four years in the 2001 cohort and at the age of three in the 2010 cohort. Logistic regression analyses were conducted. RESULTS: Children in the lowest quintile of household income were 1.54 (95% confidence interval, 1.20-1.98) times more likely to not receive center-based childcare than those in the highest-income quartile at the age of four in the 2001 cohort. Other socio-economic disadvantage (mother's low education, non-Japanese parent, and higher number of siblings) and child's health and developmental problems (preterm birth, congenital diseases, and developmental delay) were also associated with the non-use of center-based childcare at the age of three in the 2001 and 2010 cohorts. CONCLUSIONS: An inverse care law operates in the use of early childhood education (ie, children with the least need enjoy the highest access). Children with socio-economic, health, and developmental disadvantages are at a greater risk of not receiving early childhood education and care. Social policies to promote equal access to early childhood education are needed to reduce future socio-economic inequalities.