There is an association between a B region allele (here called the B' allele) of the estrogen receptor (ER) and a history of spontaneous abortion in women with ER positive breast cancer, but no such association for women with ER negative tumors or women without breast cancer. In this study we compared the heights of women carrying the B and B' alleles. The B' allele was identified by polymerase chain reaction to amplify genomic DNA around the polymorphic region of the ER gene, followed by allele specific oligonucleotide hybridization. This analysis used DNA obtained from blood lymphocytes. Women carrying the B' allele were significantly taller than those carrying the wild type allele (B allele). Multiple linear regression also demonstrated that this association remained (p = 0.017), controlling for the effects of age and race. Since the B' ER allele results from a silent mutation, a second mutation, segregating with it, no doubt plays a role in producing the high incidence of spontaneous abortion we reported previously and the height difference we report here. This second mutation might lie within the estrogen receptor itself or within one of the genes nearby.