This study was aimed at delineating molecular pathways essential in gender-different pathogenesis of chronic kidney diseases (CKD). Renal transcripts of nuclear receptors and metabolic enzymes in male and female kidneys from 5/6 nephrectomized (Nx) rats 7 weeks post-Nx were examined using branched DNA signal amplification assay. Nx-males had marked kidney injury coupled with anemia and malnutrition. Nx-females had moderate renal injury, and were free of albuminuria, anemia, and malnutrition. Nx-males had systemic and renal inflammation, which were largely absent in Nx-females. Blood 17beta-estradiol, testosterone, and corticosterone did not change, whereas urinary testosterone decreased in both genders. Compared to males, female kidneys had higher androgen receptor (AR) and aryl hydrocarbon receptor (AhR) but lower estrogen receptor alpha (ERalpha). Compared to Nx-males, female remnant kidneys had less decreases in ERalpha and peroxisome proliferator-activated receptor alpha (PPARalpha), had no induction of AR and decrease of acyl-CoA oxidase, whereas had induction of cytochrome P450 4a1 (Cyp4a1) but decrease of AhR. Renal protein expression of a 52-kDa isoform of Wilm's tumor 1 (WT1), transcription factor critical in nephrogenesis, decreased dramatically in Nx-males but largely preserved in Nx-females. In conclusion, gender divergences in basal expression and alteration of ERalpha, AR, AhR, WT1, and PPARalpha/Cyp4a1 during CKD may explain gender differences in CKD progression and outcome of renal transplantation.