BackgroundVaccination granulomas are observed in 1% of all children vaccinated with an aluminium‐adsorbed vaccine. Most children with granulomas also have aluminium contact allergy (CA). CA and atopic diseases are both highly prevalent among children and may be associated.ObjectiveTo investigate the association between vaccination granulomas and atopic dermatitis (AD), asthma and rhinitis in children.MethodsWe sourced a cohort of all Danish children born from 2009 to 2017 and conducted a nested case–control study, with cases defined as children with vaccination granulomas, matched to controls 1:10 on sex, socioeconomic class, gestational age and season of birth. All cases and controls were vaccinated with aluminium‐adsorbed vaccines and followed until their second birthday. We used conditional logistic regression to estimate the odds ratios (ORs).ResultsThe study included 2171 cases with vaccination granulomas, and 21 710 controls. Children with a diagnosis of AD had a significantly higher risk of a vaccination granuloma (OR 1.50, 95% confidence intervals [CI] 1.25–1.80). No significant association was found between granulomas and asthma or rhinitis. The association between granulomas and AD was even higher in an additional sensitivity‐analysis, following the children until their fourth birthday (OR 2.71, 95% CI 2.36–3.11).ConclusionAD was significantly associated with vaccination granulomas, but not with other atopic diseases, within both the first 2 and 4 years of life.