To estimate incidence and completeness of notification of Legionnaires' disease (LD) in The Netherlands in 2000 and 2001, we performed a capture–recapture analysis using three registers: Notifications, Laboratory results and Hospital admissions. After record-linkage, 373 of the 780 LD patients identified were notified. Ascertained under-notification was 52·2%. Because of expected and observed regional differences in the incidence rate of LD, alternatively to conventional log-linear capture–recapture models, a covariate (region) capture–recapture model, not previously used for estimating infectious disease incidence, was specified and estimated 886 LD patients (95% confidence interval 827–1022). Estimated under-notification was 57·9%. Notified, ascertained and estimated average annual incidence rates of LD were 1·15, 2·42 and 2·77/100 000 inhabitants respectively, with the highest incidence in the southern region of The Netherlands. Covariate capture–recapture analysis acknowledging regional differences of LD incidence appears to reduce bias in the estimated national incidence rate.