Trastuzumab is a humanized monoclonal antibody that is approved for the treatment of breast and gastric cancers that overexpress human growth factor receptor 2 (HER2) 3 . Since its approval, controversy has existed over whether immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH) is the best method for assessing HER2 status. Proponents of IHC point out that trastuzumab targets the HER2 protein molecule, which is assessed directly by IHC, and that the original "clinical trial assay" [and the basis of US Food and Drug Administration (FDA) clearance for the drug] was IHC. Proponents of FISH argue that IHC is more prone to technical issues (fixation, subjective interpretation, lack of proper controls on the actual procedure) and that evaluation by FISH is more objective. Although it is clear that most cases of invasive breast cancer show a direct correlation between amplification of the ERBB2 gene [v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian); also known as HER2] and overexpression of HER2 protein, IHC and FISH are complementary tests and examine different aspects of the biology of HER2-driven cancer.The accuracy of HER2 testing has generated substantial interest, especially given the poor concordance of HER2 testing results in clinical trials (1, 2 ). For example, 2 of the adjuvant clinical trials for HER2-positive breast cancer [NCCTG (North Central Cancer Treatment Group) N9831 and NSABP (National Surgical Adjuvant Breast and Bowel Project) B31] enrolled patients on the basis of a positive HER2 test result from a local laboratory, but retesting by the central laboratory revealed a negative result by both IHC and FISH in approximately 20% of the patients. These patients were still enrolled in the adjuvant trials and surprisingly demonstrated hazard ratios similar to those of patients tested as positive by IHC and FISH in the central laboratory. These findings imply that any positive test result may be predictive of benefit from trastuzumab therapy in the adjuvant setting.Contrary to widespread belief, discordance in FISH interpretations may be as common as for IHC. A recent report from the NCCTG N9831 trial (3 ) described a study in which 3 expert pathologists performed independent reads of 381 IHC samples and 373 FISH samples and obtained the same discordance rates (8%) for both IHC and FISH, even after technical standardization. These results highlight the inherent limitations of both techniques. The similar discordances between FISH and IHC are not surprising, because FISH is also subject to such preanalytical variables as cold ischemia time, type of fixative, and length of fixation, as well as analytical variables. Samples fixed in Prefer, HistoChoice, UNIFIX, and GTF, as well as delay in fixation, were associated with absent or technically compromised FISH staining (4, 5 ). Furthermore, FISH analysis is only as good as the cells that are analyzed, and identifying the invasive tumor cells can be challenging, given the presence...