Background: Children have a social status position of their own, apart from that of the family, that may have an impact on short-term and long-term health. The aim of the present study was to analyse the associations between childhood social status in school, i.e. peer status, and disease-specific morbidity in adulthood. Methods: Data was derived from a longitudinal study using a 1953 cohort born in Stockholm, Sweden: The Stockholm Birth Cohort Study (1953-2003). Peer status was sociometrically assessed in 6th grade (1966). Hazard ratios for adult disease-specific morbidity based on information on in-patient care (1973-2003) were calculated by peer status category for men and women separately, using Cox regression. Results: The results indicate that the lower the childhood peer status, the higher the overall adult disease risk. There were however differences in the degree and magnitude to which disease-specific in-patient care varied with peer status. Some of the steepest gradients were found for mental and behavioural disorders (e.g. alcohol abuse and drug dependence), external causes (e.g. suicide) and various lifestyle-related diseases (e.g. ischaemic heart disease and diabetes). The results were not explained by childhood social class. Conclusion: The present study underscores the importance of recognizing children's social position, apart from that of their family, for later health. Not only psychologically related diseases but also those related to behavioural risk factors demonstrate some of the largest relative differences by peer status, suggesting that health-related behaviour may be one important mechanism in the association between peer status and morbidity.