We have previously described three messenger RNA variants coding for the human estrogen receptor (ER) [1]. These variants were identified using the polymerase chain reaction to perform directed cloning of ER cDNAs synthesized from polyadenylated RNA extracted from the human breast cancer cell line T47D. Each of the variants is characterized by the precise deletion of a single exon within the protein coding region of this message and was presumably derived by inaccurate or promiscuous splicing of primary estrogen receptor transcripts. We report here the results of RNAse protection experiments which independently confirm the existence of these splicing variants in T47D cells. Similar analysis of RNA from MCF-7 cells also revealed the presence of variant ER transcripts, suggesting that they may be a common finding in tumor cell lines which express the estrogen receptor. However, attempts to identify splicing variants in a number of nominally ER-negative cell lines using either RNAse protection or PCR amplification were without success.