Among urological diseases, benign prostatic hyperplasia (BPH) exhibits a high morbidity rate, afflicting approximately 50% of men older than age 50 years. Despite intense research efforts over the past decades, the etiology and mechanisms of BPH progression are only poorly understood. Employing oligonucleotide microarrays, the authors analyzed the gene expression profiles in normal and BPH prostate samples and found that CYR61, an immediate early gene, is markedly overexpressed in BPH. To quantify cellular CYR61 mRNA expression directly, the authors developed an assay using branched-chain DNA (bDNA) technology. A human prostatic epithelial cell line, BRF-55T, derived from a BPH patient, was treated with fetal bovine serum to stimulate gene expression, and then the induction profile of the CYR61 mRNA in these serum-stimulated cells was quantitated using both bDNA and quantitative reverse transcriptase–PCR (RT-PCR). The results obtained with the 2 detection systems were found to be very similar. The bDNA assay was also found to be sensitive and highly reproducible. To the authors’knowledge, this is the first time that identifying CYR61 as a novel marker for BPH and its quantitation has been reported. These detection methods not only may be useful for diagnostic purposes but may also be used to identify suppressors of CYR61 expression for BPH therapy employing high-throughput screening assays.