Using microarray analysis, we have measured changes in gene expression that occurred during the evolution of a primary prostate cancer xenograft, CWR22, from normalcy to relapsed, androgen-independent growth following androgen deprivation therapy. Rather than relying on simple pairwise comparison of the data between successive biological states (for example, normal versus tumor), we clustered the expression data on the basis of behavior in multiple biological states, representative of the entire process of prostate cancer progression. By examining the data in the context of different proliferative conditions, before and after hormonal manipulation in the xenograft model, we could identify groups of genes associated with proliferation, metabolism, hormone responsiveness and malignant transformation, as well as a small number of genes directly associated with androgen-independent growth. Our results imply that the 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.