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 center dot 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 center dot 9%. Notified, ascertained and estimated average annual incidence rates of LD were 1 center dot 15, 2 center dot 42 and 2 center dot 77/100000 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.