IntroductionElectronic health records (EHRs) are increasingly used to estimate the prevalence of childhood asthma. The relation of these estimates to those obtained from parent-reported wheezing suggestive of asthma is unclear. We hypothesised that parent-reported wheezing would be more prevalent than general practitioner (GP)-recorded asthma diagnoses in preschool-aged children.Methods1529 of 1840 (83%) Millennium Cohort Study children registered with GPs in the Welsh Secure Anonymised Information Linkage databank were linked. Prevalences of parent-reported wheezing and GP-recorded asthma diagnoses in the previous 12 months were estimated, respectively, from parent report at ages 3, 5, 7 and 11 years, and from Read codes for asthma diagnoses and prescriptions based on GP EHRs over the same time period. Prevalences were weighted to account for clustered survey design and non-response. Cohen’s kappa statistics were used to assess agreement.ResultsParent-reported wheezing was more prevalent than GP-recorded asthma diagnoses at 3 and 5 years. Both diminished with age: by age 11, prevalences of parent-reported wheezing and GP-recorded asthma diagnosis were 12.9% (95% CI 10.6 to 15.4) and 10.9% (8.8 to 13.3), respectively (difference: 2% (−0.5 to 4.5)). Other GP-recorded respiratory diagnoses accounted for 45.7% (95% CI 37.7 to 53.9) and 44.8% (33.9 to 56.2) of the excess in parent-reported wheezing at ages 3 and 5 years, respectively.ConclusionParent-reported wheezing is more prevalent than GP-recorded asthma diagnoses in the preschool years, and this difference diminishes in primary school-aged children. Further research is needed to evaluate the implications of these differences for the characterisation of longitudinal childhood asthma phenotypes from EHRs.