Treatment of metastatic prostate cancer with androgen ablation often elicits dramatic tumor regressions, but the response is rarely complete, making clinical recurrence inevitable with time. To gain insight into therapy-related progression, we used microarray analysis to monitor changes in gene expression that occurred following androgen starvation of an androgen-dependent prostate tumor xenograft, CWR22, and the emergence of an androgen-independent tumor, CWR22-R. Androgen deprivation arrested the growth of CWR22 cells, as evidenced by decreased expression of genes encoding cell cycle components and basal cell metabolism, respiration and transcription, as well as the induced expression of putative negative regulatory genes that may act to sustain cells in a nonproliferative state. Evolution of androgen-independent growth and proliferation, represented by CWR22-R, was associated with a re-entry into the active cell cycle and the upregulation of several genes that were expressed at low levels or absent in the androgen-dependent tumor. Restoration of androgen to mice bearing androgen-independent CWR22-R tumors induced, augmented or repressed the expression of several androgen-responsive genes. Two of the genes whose expression was increased by androgens (the calcium-binding protein, S100P, and the FK-506-binding protein, FKBP51) were also expressed in CWR22-R. The dysregulated behavior of these genes is analogous to that of other androgen-dependent genes (for example, prostate-specific antigen and human kallikrein 2), which are commonly re-expressed in androgen-independent disease in the absence of androgens. These results imply that evolution to androgen independence is due in part to reactivation of the androgen response pathway in the absence of androgens, but that this reactivation is probably incomplete.