Overall management of quality control for clinical gene amplification test should be considered as an extension operation of traditional laboratory quality control system. It should initiate from the design of laboratory layout to the process of laboratory construction to emphasize the overall plan. To ensure the quality of pre-analysis management, the quality of specimen should be monitored carefully and all the information and data should be managed by utilizing computerized system. During analytic process, the operational compliance should be strengthened to ensure a correct operation. Then, verification procedure for the result should be standardized, and the effectiveness of the test should be carefully evaluated. In addition, the effective communication between laboratory staff and clinician should be established. In sum, to ensure the clinical significant of results, clinical gene amplification test should be managed carefully from the laboratory design to each step of test practice including the post-analysis and discussion with clinician.