Previous analysis of in utero dibutylphthalate (DBP)-exposed fetal rat testes indicated that DBP's anti-androgenic effects were mediated in part by indirect inhibition of SF1 suggesting that PPARα might be involved through coactivtor (CBP) sequestration. To test this hypothesis we have performed ChIP microarray analysis to assess the DNA-binding of PPARα, SF1, CBP and RNApol11 in dibutylphthalate-induced testicular mal-development target genes. Pathways analysis of expression array data in fetal rat testes examined at GD15, 17 or 19 indicated lipid metabolism genes regulated by SF1 and PPARα, respectively, were over-represented and the time-dependency of changes to PPARα-regulated lipid metabolism genes correlated with DBP-mediated repression of SF1-regulated steroidogenesis genes. ChIP microarrays were used to investigate whether DBP-mediated repression of SF1-regulated genes was associated with changes in SF1 binding to genes involved in dibutylphthalate-induced testicular mal-development. DBP-treatment caused reductions in SF1 binding in CYP11a, StAR and CYP17a. FSHR, regulated by SF1 but unaffected by DBP-treatment, also contained SF1 binding peaks, but DBP did not change this compared to control. GD15 and GD19 fetal testes contained PPARα protein-binding peaks in CYP11a, StAR and CYP17a regulatory regions. In contrast to its repressive effect on SF1, DBP-treatment caused increases in these peaks compared to control. PPARα binding-peaks in the FSHR promoter were not detected in GD15 samples. Hence the repressive effect of DBP on SF1 regulated steroidogenic genes correlates with inhibition of SF1-DNA binding and increased PPARα-DNA binding. The data indicate that PPARα may act as an indirect transrepressor of SF-1 on steroidogenic genes in fetal rat testes in response to DBP treatment.