Diseases are increasingly being defined in terms of genetic alterations. A body of information termed "molecular pathogenesis" is evolving which provides a framework for integrating the rapidly accumulating genetic information with the related disease process. Molecular methods with their increased sensitivity and specificity are required to gather this information. A major challenge now lies in the transfer of this molecular technology from a research environment to the clinical testing arena. Technical issues, patented technology, special facilities, personnel, and regulatories issues imposed by CLIA'88, require those desiring to perform molecular tests to pay special attention to laboratory design, personnel training, and test menu development. Although establishing a successful molecular diagnostics laboratory is a complex and difficult task, the added value of these tests can have a tremendous impact in disease diagnosis and patient management.