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Recent data suggest that molecular diagnosis of pneumococcal disease may finally be ready for general use in patients with community-acquired pneumonia. In addition to vastly improved sensitivity and a high specficity, a new pneumococcal assay also quantitates the bacterial load in blood. This review discusses the primary and supporting data, along with the current limitations and likely future developments. This review also focuses on the new opportunities presented by this assay for improving the outcome of patients with community-acquired pneumonia, and the implications for the pathogenesis of severe sepsis in pneumococcal pneumonia.