Tumor response and toxicities are different among individual patients. Pharmacogenomics studies aim to elucidate the genetic bases for interindividual differences and to allow individualization of care, using the knowledge of molecular biology, recently developed high-throughput biotechnology and bioinformatics. Transcription profiling of gene expression have been extensively studied in breast cancer. Breast cancer may be re-subclassified into subtypes according to molecular profiles with distinct differences in prognosis and response to therapy. Although there still lay problems in standardization of methodology and statistical validation, genomics studies have the potential to play the key role in the development of novel therapeutical strategies in the management of breast cancer.