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We aimed to study growth during the first 2 years of life in children later diagnosed with coeliac disease compared with children without, in a time with changing epidemiology and improved diagnostics.A prospective population-based pregnancy cohort study.The nationwide Norwegian Mother and Child Cohort Study.58 675 children born between 2000 and 2009 with prospectively collected growth data. Coeliac disease was identified through combined data from questionnaires and the Norwegian Patient Register.The differences in height and weight at age 0, 3, 6, 8, 12, 15–18 and 24 months using internally standardised age and gender-specific z-scores. Linear regression and mixed models were used.During a median follow-up of 8.6 years (range 4.6–14.2), 440 children (0.8%) were diagnosed with coeliac disease at a mean age of 4.4 years (range 1.5–8.5). Children with coeliac disease had significantly lower z-scores for height from 12 months (−0.09 standard deviation scores (SDS), 95% CI −0.18 to −0.01) and weight from 15 to 18 months of life (−0.09 SDS, 95% CI −0.18 to −0.01) compared with cohort controls. The longitudinal analysis from 0 to 24 months yielded a significant reduction in height z-score per year (−0.07 SDS, 95% CI −0.13 to −0.01) but not for weight among children with coeliac disease. Excluding children diagnosed before age 2 years gave similar results.This study indicates that growth retardation in children later diagnosed with coeliac disease commonly starts at 12 months of age, and precedes clinical symptoms that usually bring the suspicion of diagnosis.