Two novel transcripts of human estrogen receptor (ER) have been identified that differ in the 5' untranslated sequence. It has previously been determined that an alternate ER transcript is generated from transcription initiated upstream of the main ER cap site (P1), and utilizes a splice acceptor site at +163. Here we report the isolation of 21 ER clones from a MCF7 cDNA library. Eleven of these clones correspond to transcripts that initiate at the P1 cap site, whereas the remaining 10 clones are derived from two previously unidentified ER transcripts (designated E and H) that both utilize the +163 splice acceptor site. A panel of breast and endometrial carcinoma cell lines were screened by reverse transcriptase-polymerase chain reaction (RT-PCR) for expression of the E and H transcripts. It was found that all ER-positive cell lines expressed both of the novel transcripts. In addition, 10 primary human breast cancers were analyzed, of which six expressed the E transcript and five abundantly expressed the H transcript. These data indicate that expression of ER in human breast cancers can be dependent upon an alternate promoter at least 20 kb upstream of the primary cap site for ER.