DNA from ninety-eight primary breast cancer biopsies has been examined for loss of heterozygosity (LOH). Thirteen of seventy-two informative cases (18.1%) were positive for LOH, which correlated with age at operation but not with ER status. This result suggests that LOH of the ER gene does not have an important role in the lack of ER function in breast cancer tissues. Thirteen breast cancers with ER negative/progesterone receptor (PgR) positive were screened for mutation analysis of the ER gene using single strand conformational polymorphism (SSCP). We found 2 polymorphisms in codon 10 (C to G) codon 325 (C to T), although neither germline nor somatic mutation was detected. Since the sequence variant of codon 325 tends to be more frequently seen in ER negative/PgR negative breast cancer patients than non-cancer control patients, it is suggested that this polymorphism was related to negativity and function of ER in breast cancer tissues.