This archived document is no longer being reviewed through the CLSI Consensus Document Development Process. However, this document is technically valid as of January 2020. Because of its value to the laboratory community, it is being retained in CLSI's library.Nucleic acid methods for the detection and characterization of microorganisms in clinical specimens are now firmly established in laboratory medicine. These methods offer opportunities for clinical laboratories to provide more rapid and accurate results, and have changed the practice of clinical microbiology and infectious diseases. Clinical and Laboratory Standards Institute document MM03—Molecular Diagnostic Methods for Infectious Diseases addresses topics relating to clinical applications, amplified and nonamplified nucleic acid methods, selection and qualification of nucleic acid sequences, establishment and evaluation of test performance characteristics, inhibitors, and interfering substances, controlling false-positive reactions, reporting and interpretation of results, QA, regulatory issues, and recommendations for manufacturers and clinical laboratories.