Denmark has in the past 10 years experienced a decrease in the number of notified cases of meningococcal disease. In 1994 the completeness of the Notification System for Meningococcal Disease (NSMD) was estimated as 96% (95% CI 93-98). To answer the question whether the observed decrease reflects a real decrease in the incidence; we estimated the completeness of the notification system in 2002. We estimated the completeness of registration by a capture-recapture analysis. As the first data source, we used the national NSMD, which is an integrated surveillance system between the Department of Epidemiology and the Neisseria Reference Laboratory. The second independent source was the National Patient Registry (NPR). In 2002, the completeness of the NSMD was estimated as 96% (95% CI 95-98) and for the NPR as 84% (95% CI 82-85). The 'real' incidence rate was 1.9/100 000 population, which compared to 4.4/100 000 population in 1994. We concluded that the observed decrease in incidence rate is real. The NSMD in Denmark functions well and captures almost all cases of meningococcal disease. The complete registration which includes a unique personal identification number serves as an outstanding source for nationwide registry linkage studies.