BACKGROUND: The lack of comprehensive food composition databases for sugar contents in Japanese foods has led to the lack of nutritional epidemiologic studies on sugar intake in Japanese population. This cross-sectional study aimed to investigate the association of free sugar intake estimated using a newly developed food composition database with the characteristics and lifestyles of Japanese children aged 3-6 years. METHODS: The food composition database contained information on sugars in 2,222 commonly consumed Japanese foods. Using this database, we estimated the sugar (total, added, and free sugars) intakes derived from a 3-day weighed dietary record of 166 boys and 166 girls aged 3-6 years living in 24 prefectures in Japan. RESULTS: The mean free sugar intake was 26.8 g/d (standard deviation [SD], 12.3 g/d), while the mean value for energy intake was 7.8% (SD, 3.2%). The prevalence of excessive free sugar intake (≥10% of energy intake) was 21.7%. Among the characteristics and lifestyles examined, screen time was most strongly associated with the prevalence of excessive free sugar intake: multivariate adjusted odds ratios for screen time <0.5, ≥0.5 to <1, and ≥1 h/d were 1.0 (reference), 3.81 (95% confidence interval, 1.04-13.98), and 4.36 (95% confidence interval, 1.16-16.35), respectively. Additionally, younger age, shorter sleep, and mothers with office work and service and sales jobs (compared with those with professional and managerial jobs) were significantly associated with a higher prevalence of excessive free sugar intake. CONCLUSIONS: This study showed the sugar intake of Japanese children aged 3-6 years is positively associated with screen time.