Androgens are essential for the development and maintenance of spermatogenesis but the underlying mechanisms of androgen action in the testis remain unclear. To help clarify these mechanisms, gene expression was measured in testes of pubertal (20 day old), androgen-insensitive, testicular feminised (Tfm) mice and in normal controls. Using microarrays (Affymetrix chips 430A and 430B) initial data identified a large number of genes down-regulated in the Tfm testis (>4700). These genes were largely of germ cell origin, reflecting the arrest of spermatogenesis which is apparent in the 20 day old Tfm testis. Subsequent screening in vitro and in silico of this gene set identified 20 genes of a somatic tubular origin which were significantly downregulated in the Tfm testis and 6 genes which were significantly upregulated. Altered expression of these genes was confirmed by real-time PCR and genes down-regulated in the Tfm testis were shown to be up-regulated in testes of hypogonadal (hpg) mice treated with androgen. In a developmental study using real-time PCR most of the regulated genes showed normal expression during fetal and neonatal development and only deviated from control between 10 and 20 days. In all cases expression was also reduced in the adult although interpretation is more complex because of the inherent cryptorchidism in the adult Tfm mouse. Of the total number of somatic genes showing differential expression in the Tfm testis, 50% were associated with three separate groups of genes involved in regulation of vitamin A metabolism, solute transportation and cytoskeletal function. Thus, effects of androgens on tubular function and spermatogenesis may be mediated in part through regulation of the tubular environment and control of retinoic acid concentrations.