The purpose of this study was to describe gender differences in children's health until the age of 7 y. The study cohort consisted of all children born in Finland in 1987 (n = 60254), of whom 99.9% were identified in the follow-up. Childhood health data were received from five national registers (1987-94), from regional registers of intellectual disabilities (1987-96) and from education registers in the largest county (1996). Boys had a 20% higher risk for a low 5-min Apgar score and an 11% higher risk for being preterm. After the perinatal period, boys had a 64% higher cumulative incidence of asthma, a 43% higher cumulative incidence of intellectual disability, a 22% higher incidence of mortality and a higher, but not statistically significant, incidence of epilepsy and vision disorders. No male excess was found for diabetes or hearing disorders. The healthcare-related indicators showed poorer health for boys, who had a 37% higher mean of hospital days, a 28% higher risk for receiving social benefits due to health problems and a 13% higher risk for long-term medication. The differences in the socially defined indicators were greatest, and boys had a two- to three-fold risk of having delayed development, postponed school start or attendance in special education programmes. Gender differences in different social classes were similar. Boys' shorter gestational age at birth did not explain the gender differences in childhood health. Some of boys' poorer health seemed to be biologically based, but the social causes of health problems are amenable to change. In particular, the potential of the school system to reduce ill health among boys should be investigated.