Molecular diagnostics has become one of the dominant platforms in clinical laboratory medicine. Technological improvements, from automated sample preparation to real time amplification technology, provide the possibility to develop and run assays for a growing number of clinical questions. However, quality assurance and quality control issues have often remained underdeveloped but are still critical. To relate patient results to prior results or to absolute values in clinical practice guidelines, those results need to be comparable across time and methods. This may be achieved either by producing the identical value across methods and test versions or by using reliable and stable conversions. The establishment of international standards and reference materials is thus of paramount importance. This review focuses on general and specific issues relevant for quality assurance and quality control in the routine molecular diagnostics laboratory.