The introduction of targeted cancer therapies into clinical practice, in which patients are selected for novel treatments based on results of companion molecular testing of their tumor specimens, has created significant new challenges for the surgical pathology laboratory. These include standardization of tissue handling and sample preparation with accurate documentation to ensure optimal quality of clinical samples to reduce the risk of errors in molecular biology tests. The assay of tumor tissues for biomarkers that can provide predictive data for prognosis or treatment should enable selection of the most appropriate therapies (Yaziji et al. 2008, Hicks and Kulkarni 2008). Major advances have been made in the ability to profile clinical samples for research at the DNA, RNA and protein levels. To translate this new information into the clinical setting, however, the quality of the starting material, in this case the tumor tissue, determines the accuracy and reliability of companion diagnostic assay results and therefore optimal therapeutic strategies. Inaccurate results owing to compromised tissue quality can lead to false positive or false negative results with therapeutic consequences that can harm patients and affect their eventual outcome.