Community-level social environment has been considered to be associated with smoking behavior. However, no study has examined the association between community-level environmental factors and parental smoking behavior in families with young children. The aim of the present study was to examine the association between community-level socioeconomic status (SES) and parental smoking behavior. We used data from a cross-sectional study conducted from 2005 to 2006. We randomly selected 44 Japanese municipalities, 39 of which municipalities agreed to participate in this survey. The study subjects were participants in health check-ups for three-year-old children. Smoking status and individual demographic characteristics were obtained using self-administered questionnaires. Community-level variables were obtained from national census data for 2005. The prevalence of employment in tertiary industries and of unemployment was used to measure community-level SES. Multilevel Poisson regression models were used to calculate prevalence ratios (PRs) for smoking. Of 4143 subjects, a total of 3301 parents in 39 municipalities participated in our survey. Among the 2975 participants (71.8%) included in our analysis, 59.0% were smokers. There was no association between the job of the head of the household considered as an indicator of individual-level SES and smoking. By contrast, when we examined the relationship between prevalence of employment in tertiary industries as community-level SES and smoking, parents living in low middle SES municipalities had a significantly higher prevalence ratio for smoking, compared to parents living in the highest SES municipalities. This result suggested that those with lower community-level SES tended to have a higher prevalence of parental smoking regardless of individual-level SES.