Severe early childhood caries (S-ECC) has serious consequences for primary dentition, affecting the overall health, well-being, and quality of life of the child. The aim of this study was to investigate the association of risk factors, including environmental tobacco smoke (ETS), with S-ECC in 3-year-old Japanese children by a cross-sectional study. Study subjects were 2,825 children aged 3 years old. Of these individuals, after excluding the study subjects with missing values, a total of 2,277 children were included in the present analysis. The self-administered questionnaire included such items as sex, whether a smoker resides in the home, the number of smokers in the home, snack time, drinking or eating sweets after dinner, frequency of parents brushing their child’s teeth, the use of fluoride toothpaste, and socioeconomic status. We obtained the number of decayed, missing, or filled teeth per person (dmft) from dental examinations. Logistic regression analysis was performed to estimate the odds ratio for S-ECC. The average number of decayed, missing, and filled teeth (dmft index) was 0.77. The prevalence of dental caries was 20.6%. There was at least 1 smoker in the homes of 1,370 subjects (60.2%). After excluding items of multicollinearity, the results of multivariate analysis were as follows: drinking or eating sweets after dinner, irregular snack times, parents brushing their child’s teeth less frequently, existence of smokers in the home, and no residence tax were significantly associated with S-ECC. This study suggests that there is a significant association between ETS from family members and S-ECC.

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