The human glucocorticoid receptor (GR) gene produces C-terminal GRbeta and GRalpha isoforms through alternative use of specific exons 9beta and alpha, respectively. We explored the transcriptional activity of GRbeta on endogenous genes by developing HeLa cells stably expressing EGFP-GRbeta or EGFP. Microarray analyses revealed that GRbeta had intrinsic gene-specific transcriptional activity, regulating mRNA expression of a large number of genes negatively or positively. Majority of GRbeta-responsive genes was distinct from those modulated by GRalpha, while GRbeta and GRalpha mutually modulated each other's transcriptional activity in a subpopulation of genes. We did not observe in HCT116 cells nuclear translocation of GRbeta and activation of this receptor by RU 486, a synthetic steroid previously reported to bind GRbeta and to induce nuclear translocation. Our results indicate that GRbeta has intrinsic, GRalpha-independent, gene-specific transcriptional activity, in addition to its previously reported dominant negative effect on GRalpha-induced transactivation of GRE-driven promoters.