Sleep problems are highly prevalent in ADHD and autism spectrum disorder (ASD). Better insight in the etiology is of clinical importance since intervention and prevention strategies of sleep problems are directed at underlying mechanisms. We evaluated the association of sleep problems and sleep patterns with sleep hygiene (behavioral/environmental practices that influence sleep quality, e.g. caffeine use), access to electronic media, chronotype, and anxiety/depression in children aged 6–12 years with ADHD, ASD, or typical development (TD) using parental questionnaires. ANOVA and linear regression analyses were adjusted for age and sex. Children with ADHD and ASD showed more sleep problems (63.6 and 64.7%, vs 25.1% in TD) and shorter sleep duration than controls, while differences between ADHD and ASD were not significant. Sleep hygiene was worse in ADHD and ASD compared to TD, however, the association of worse sleep hygiene with more sleep problems was only significant in ASD and TD. There was a significant association of access to electronic media with sleep problems only in typically developing controls. Chronotype did not differ significantly between groups, but evening types were associated with sleep problems in ADHD and TD. Associations of greater anxiety/depression with more sleep problems were shown in ADHD and TD; however, anxiety/depression did not moderate the effects of chronotype and sleep hygiene. We conclude that sleep problems are highly prevalent in ADHD and ASD, but are differentially related to chronotype and sleep hygiene. In ASD, sleep problems are related to inadequate sleep hygiene and in ADHD to evening chronotype, while in TD both factors are important. Clinical implications are discussed.