The first stage of early childhood caries (ECC) is infection by mutans streptococci, of which the primary infection source is the child's mother. Early intervention programs including antenatal and postnatal phases are effective for reducing ECC. This study was conducted to assess the respective effects of antenatal health care and postnatal care such as regular dental check-ups on reducing ECC among 3-year-old Japanese children. This nested case-control study of 155 three-year-old children (49.0% boys) was conducted at a dental clinic that provides collaborative health services with the Obstetrics and Gynecology Clinic, Okayama. Child characteristics and the mothers' antenatal data were collected retrospectively from the dental charts. They were divided into two groups: caries-free children (n = 77) and children without ECC (n = 78). Most of the children (81.9%) received regular check-ups with topical fluoride application. Most of the mothers reported morning sickness during pregnancy (81.3%), normal delivery (72.9%), and used antenatal health care (80.6%). Over half (55.5%) were primigravida. Adjusted odds ratio (AOR) and 95% confidential interval (95% CI) were computed to assess the strength of association using logistic regression analysis. Receiving antenatal health care (AOR, 3.27; 95% CI,) and child's having regular check-ups (AOR, 3.42; 95% CI, 1.35-8.69) were significantly associated with caries-free status among three-year old children. For ECC prevention, antenatal health care is as effective as regular check-ups up to three years of age. The results of this retrospective study demonstrate that maternal health education during pregnancy is effective for ECC prevention.