The purpose of this study was to investigate the relationships between sleep onset latency (SOL) and other sleep-wake patterns and media use habits in Japanese schoolchildren. A total of 9,718 junior high school children responded (12.8 years) and 9199 questionnaires were used in the present analyses. The questionnaire assessed sleep-wake patterns, TV viewing and videogame habits. Overall, 72.1% of the subjects reported short SOL (<or=20 min). Long SOL subjects (>20 min) were strongly associated with disturbed sleep manifested especially by increased risk of night awakenings, decreased sleep depth, and bad sleep in general (overall sleep quality). Prolonged SOL was also associated with daytime sleepiness, difficulties in falling asleep, bad morning feeling and sleep insufficiency. We found a U-shaped relationship between sleep period and SOL. Increase in bedtime was accompanied by increased risk of prolonged SOL. The impact of ultra-short and ultra-long SOL (<or=5 and >or=40 min) was also analysed. Long durations of watching television and playing videogame were significantly associated with prolonged SOL. After adjustment for sex, girls presented significantly higher risk of prolonged SOL. Body mass index adjustment did not reveal any significant results. SOL presents a significant component of sleep-wake habits; poor sleep hygiene and insufficient sleep time significantly increase SOL. Parents, healthcare practitioners and children themselves should be aware of the potentially negative influence of prolonged SOL. Additionally, the optimal coherent sleep-wake schedule must be promoted in parallel with the limitation on the viewing TV and game practices.