Coeliac disease might affect school performance due to its effect on cognitive performance and related health consequences that might increase school absenteeism. The aim of this study was to investigate whether children with coeliac disease performed differently on completion of ninth grade in school compared with children without coeliac disease.Analysis was performed on a population of 445 669 children born in Sweden between 1991 and 1994 of whom 1767 were diagnosed with coeliac disease. School performance at ninth grade was the outcome and coeliac disease was the exposure. Other covariates included sex, Apgar score at 5 min, small for gestational age, year of birth, family type, parental education and income.There was no association between coeliac disease and school performance at ninth grade (adjusted coefficient -2.4, 95% CI 5.1 to 0.4). A weak association was established between late coeliac diagnosis and higher grades, but this disappeared after adjusting for parent socioeconomic conditions. Being small for gestational age affected performance negatively (adjusted coefficient -6.9, 95% CI 8.0 to 5.7). Grade scores were significantly lower in children living with a single parent (adjusted coefficient -20.6, 95% CI 20.9 to 20.2), compared with those with married/cohabiting parents. A positive association was found between scores at ninth grade and parental education and income.Coeliac disease diagnosis during childhood is not associated with poor school performance at ninth grade.