Estrogen receptor (ER) status of breast cancer can be assessed by immunohistochemical assay (IHA), although we have previously observed that ER-IHA levels can be inconsistent between amino-terminal and carboxyl-terminal-targeted antibodies. To address the hypothesis that this discrepancy is attributable to expression of ER variant mRNAs encoding truncated ER-like proteins, we have studied 39 IHA-consistent and 24 IHA-inconsistent breast tumors by reverse transcription polymerase chain reaction to examine the expression of multiple exon-deleted (D-ER) variant mRNAs and the truncated ER clone 4 variant mRNA. ER variants D7-ER, D-3-4-ER, and D4-7-ER were detected at similar frequencies in both groups. However, ER variants D2-3/7-ER, D2-3-4-ER (P < 0.05), and D-3-7-ER (P < 0.01), which encode putative short ER-like proteins that might be recognized only by an amino-terminal-targeted antibody, were preferentially detected in inconsistent cases. ER clone 4 mRNA expression was also higher in inconsistent tumors (P < 0.001). Further analysis showed that, whereas overall prevalence of ER variant mRNAs was similar in both tumor groups, occurrence of the subset of variant mRNAs encoding putative truncated proteins was also higher in IHA-inconsistent tumors (P < 0.05). These data suggest that ER variant mRNAs encoding truncated ER proteins may contribute to discrepancies in ER-IHA levels determined using amino- or carboxyl-terminal-targeted antibodies.