Estrogen receptor (ER) content is a well-known predictor of clinical outcome in human breast cancer. The recent cloning of a human ER complementary DNA has made possible the characterization of the ER gene on a molecular level. We have examined in human breast cancers a single, two-allele restriction fragment length polymorphism using the restriction enzyme PvuII. Initial studies in human breast cancer cell lines suggested a possible association between the absence of one allele and the absence of ER expression; subsequent analysis of allele distribution and frequency in 188 primary human breast tumor biopsies did indeed show a significant but not complete correlation between the absence of one allele and the failure to express ER. Preliminary data suggest that this restriction fragment length polymorphism is located within gene sequences coding for the putative DNA or hormone-binding domains of the ER.