Previous analysis of in utero dibutylphthalate (DBP)-exposed fetal rat testes indicated that DBP's antiandrogenic effects were mediated, in part, by indirect inhibition of steroidogenic factor 1 (SF1), suggesting that peroxisome proliferator-activated receptor alpha (PPARα) might be involved through coactivator (CREB-binding protein [CBP]) sequestration. To test this hypothesis, we have performed chromatin immunoprecipitation (ChIP) microarray analysis to assess the DNA binding of PPARα, SF1, CBP, and RNA polymerase II in DBP-induced testicular maldevelopment target genes. Pathway analysis of expression array data in fetal rat testes examined at gestational day (GD) 15, 17, or 19 indicated that lipid metabolism genes regulated by SF1 and PPARα, respectively, were overrepresented, 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 DBP-induced testicular maldevelopment. DBP treatment caused reductions in SF1 binding in CYP11a, StAR, and CYP17a. Follicle-stimulating hormone receptor (FSHR), regulated by SF1 but unaffected by DBP-treatment, also contained SF1-binding peaks, but DBP did not change this compared with 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 with 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 SF1 on steroidogenic genes in fetal rat testes in response to DBP treatment.