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To assess the longitudinal effects of sleep duration and quality on lipid profiles during the transition from childhood to early adolescence, over a 4-year-period.A cohort study of children born in 1998 examined at 8 years of age (SD, 0.3; n = 105) and 12 years of age (SD, 0.5; n = 190). Sleep duration, wake after sleep onset, sleep efficiency, and weekend catch-up sleep were measured with actigraphs for 7 (8 years of age) and 8 (12 years of age) nights. Fasting serum samples were collected at 12 years of age. Covariates included age, pubertal development, socioeconomic status, body mass index, and physical activity.In girls, shorter sleep duration at 8 and 12 years of age was associated with lower high-density lipoprotein-cholesterol and higher triglycerides at 12 years of age. Poorer sleep quality at 8 years of age and longer weekend catch-up sleep at 12 years of age was associated with higher triglycerides at 12 years of age. From 8 to 12 years of age, improvement in sleep quality associated with higher total cholesterol, and a decrease in sleep duration with lower lipid levels. In boys, longer sleep duration at 8 years of age, and a larger decrease in sleep duration from 8 to 12 years of age was associated with higher levels of triglycerides at 12 years of age.Poorer sleep during transition to early adolescence is associated with an atherogenic lipid profile in early adolescent girls, and such effects are less prominent in boys. Poor sleep may have long-term associations with health, which are not mitigated by the amount of physical activity.