Background: The aim of this study was to compare prevalence estimates of asthma or chronic obstructive pulmonary disease (COPD) derived from self-report in a health interview survey and from general practitioners' (GPs') medical records, and to explain any differences. Methods: the presence of asthma or COPD was measured by self-report in a random sample of 104 general practices in the Netherlands (n = 19 685) participating in the second Dutch National Survey of General Practice (DNSGP-2). This was compared with the presence of GP-diagnosed asthma or COPD in the same population as recorded using the International Classification of Primary Care by their GPs during a 12-month period. Gender, age, health insurance, ethnic background, educational level, tobacco exposure, and other symptoms and conditions were evaluated as explanatory variables using logistic models. Results: The prevalence of self-reported asthma or COPD (9.7%) was almost twice as high as the prevalence based on GP information (5.2%). The medical records of patients who reported having asthma or COPD, without having a diagnosis in their medical records, usually included other respiratory conditions. Patients reporting no asthma or COPD but whose medical records carried a diagnosis of asthma or COPD, were relatively older (P < 0.01) and tended to be exposed to smoking in their home (P < 0.05). Conclusions: Two methods for estimating prevalence of asthma or COPD yielded different results: compared with GP medical records, self-reported prevalence shows an overestimation in people who suffer from other respiratory conditions and an underestimation in elderly persons living in a smoky environment.