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Diagnosis of chlamydial and gonococcal infections is the foundation of most sexually transmitted infection control programs. Early detection and treatment of disease is essential for disruption of transmission. DNA-based assays have been shown to have the highest available sensitivity and specificity but are often time-consuming and technically demanding. The COBAS Amplicor is an automated system that performs a combined chlamydia and gonorrhea diagnostic assay suitable for use in either public health or reference laboratories.