We evaluated the differences in prevalence and functional activity of human estrogen receptor alpha (hER) variant mRNA between 21 normal breast tissues and 41 primary breast carcinomas using a functional assay in yeast for the hER First, we found that the presence of wild-type hER, relative to the total amount of hER, differs markedly (P < 0.0001) between normal breast tissue (median, 85% wild-type hER) and breast tumors (median, 74% wild-type hER). Second, the hER variants with altered function that are present in normal breast tissue are mainly one-exon deleted splicing variants (median, 100%), whereas in breast tumors only half of all variants lack just one single exon (median, 50%; P < 0.0001). Our results suggest that hER-dependent estrogen responsiveness of breast tissue may change during tumor outgrowth, indicating that specific hER variants may play a role in breast cancer development or progression.