To detect patients with poor prognosis among those with estrogen receptor (ER)-positive breast cancer, who generally show good prognosis, we analyzed gene expression profiles of 35 ER-positive tumors by using a high through-put RT-PCR technique, iAFLP. High expression of six genes out of 7,508 was related to poor prognosis in this group. From these six genes, NFE2L2 and TIAL1 were selected as genes associated with poor prognosis by means of a validation study with another set of 56 ER-positive breast cancers. High expression of these two genes was determined to be significantly predictive for poor prognosis of patients with ER-positive breast cancer, and may help to achieve optimal selection of adjuvant treatment for such patients.