While the importance of social relations for health has been demonstrated in childhood, adolescence and adulthood, few studies have examined the prospective importance of peer relations for adult health. The aim of this study was to examine whether peer problems in the school setting in adolescence relates to the metabolic syndrome in middle-age. Participants came from the Northern Swedish Cohort, a 27-year cohort study of school leavers (effective n = 881, 82% of the original cohort). A score of peer problems was operationalized through form teachers' assessment of each student's isolation and popularity among school peers at age 16 years, and the metabolic syndrome was measured by clinical measures at age 43 according to established criteria. Additional information on health, health behaviors, achievement and social circumstances were collected from teacher interviews, school records, clinical measurements and self-administered questionnaires. Logistic regression was used as the main statistical method. Results showed a dose-response relationship between peer problems in adolescence and metabolic syndrome in middle-age, corresponding to 36% higher odds for the metabolic syndrome at age 43 for each SD higher peer problems score at age 16. The association remained significant after adjustment for health, health behaviors, school adjustment or family circumstances in adolescence, and for psychological distress, health behaviors or social circumstances in adulthood. In analyses stratified by sex, the results were significant only in women after adjustment for covariates. Peer problems were significantly related to all individual components of the metabolic syndrome. These results suggest that unsuccessful adaption to the school peer group can have enduring consequences for metabolic health.