BACKGROUND: The nuclear receptor genes, including estrogen receptor β (ERβ), contain non-conventional internal and terminal exons, and alternative choice of the exons yields multiple mRNA and protein variants with unique structures and functions. However, the genomic structure of the intronic and 3'-downstream regions of the human ERβ gene and the presence of novel ERβ variants with non-conventional sequences have not been re-examined in about 20 years. Therefore, we attempted to re-characterize the structure of the human ERβ gene and identify novel non-conventional exons and distinct splice variants. METHODS: Rapid amplification of cDNA 3'-end and RT-PCR cloning were used to isolate human ERβ mRNA variants from the testis. The identified cDNA sequences were mapped on the human genome assembly. Expression profiles of the variants were assessed by RT-PCR analysis. RESULTS: We cloned multiple ERβ mRNA variants with novel nucleotide sequences from the testis and identified several alternative splice sites, 3'-elongation of conventional coding exons, and novel terminal exons in the human ERβ gene. The variants encode C-terminally truncated ERβ proteins termed ERβ6, ERβ7, ERβEx. 4L, and ERβEx. 6L. Furthermore, we identified exon 7-defective forms of ERβ2/βcx, ERβ4, ERβ6, and ERβ7. Subsequently, we noted distinct expression patterns of the variants in human peripheral organs and brain subregions. CONCLUSION: This study clarified complicated genomic organization and splicing patterns of the human ERβ gene that contribute to the distinct heterogeneity of human ERβ mRNAs and proteins.