Previously we have reported an increased nuclear estrogen receptor-alpha (ERalpha) in the medial mamillary nucleus (MMN) in Alzheimer's disease (AD). In the present study, we addressed the presence of specific ERalpha mRNA splice variants in this brain area of five AD cases compared with five controls using the RT-PCR and quantitative RT-PCR approach. Indeed, the occurrence of isoforms with the deletion of exons 7 (del.7), 4 (del.4), or 2 (del.2) was determined in all patients. However, there were no significant differences in the relative transcription levels of each of the mentioned splice variants between AD and control cases, although the ratio of the del.7 isoform to the canonical ERalpha mRNA was higher in controls. Given that exons 7 and 4 encode the ligand-binding domain of the ERalpha, whereas exon 2 encodes the DNA-binding domain, abundant expression of these splice variants suggests that much of the available ERalpha in the MMN of AD and elderly control patients is nonfunctional because they will be unable to bind either the ligand (del.7 and del.4 variants) or the estrogen-responsive elements on appropriate DNA (del.2 variant). Yet, the wild-type ERalpha mRNA appeared to be 2- to 3-fold up-regulated in AD, confirming the rise in the nuclear immunocytochemical staining and pointing to the potential for a beneficial effect of estrogen replacement therapy on the MMN-associated cognitive functions in AD because it represents the availability of potentially functional ERalpha in the MMN. Noteworthy, the expression of the wild-type, del.7, and del.2 mRNAs declined with advanced age in both AD and control patients. Interestingly, we have identified in two AD and two control patients a novel ERalpha splice variant that we called MB1 (mamillary body, exon 1) with a 168-nucleotide deletion corresponding to a U2-type intron inside exon 1 encoding the major portion of the transactivation function 1 domain of the receptor.