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The aim of this study was to determine the incidence of pneumococcal endocarditis in 3 Danish counties. By linking the National Hospital Discharge Registry to regional blood culture registries maintained by the Department of Clinical Microbiology and autopsy registries from the Department of Pathology, a total of 31 cases of pneumococcal endocarditis was identified in the 3 counties during a period of 16 y (1981–1996). One patient experienced 2 independent episodes as determined by serotyping. The annual incidence increased approximately 4-fold during the study period, giving an overall incidence rate of 0.15 per 100,000 inhabitants. Pneumococcal endocarditis was diagnosed in 1.2% of cases of pneumococcal bacteraemia. Some cases may have remained undetected, and this underlines the need for clinical attention to this diagnosis. The study confirms that linkage of health registries is a valid method of conducting surveys of uncommon diseases.