Chemotherapy plays an important role in cancer therapy. The major problem of chemotherapy is that only a part of patients can receive benefit of chemotherapy. The low efficacy of cancer chemotherapy is mostly due to heterogeneity in cancers. Recent advance in molecular biology has made possible to analyze expressions of a large number of genes simultaneously. To identify cancers effective in the chemotherapy, differences in signatures of genes expressions are compared between in chemotherapy effective cancer and in ineffective ones. Such attempts have been applied to molecular diagnostic tools to predict clinical outcome of the cancer. Using such tools, individualization of cancer chemotherapy is now on clinical trial. In this article, we review molecular diagnostic tools focusing on breast cancer therapy.