Conventional biochemical and molecular techniques identified previously several genes whose expression is regulated by the aryl hydrocarbon receptor (AHR). We sought to map the complete spectrum of AHR-dependent genes in male adult liver using expression arrays to contrast mRNA profiles in Ahr-null mice (Ahr Ϫ/Ϫ ) with those in mice with wild-type AHR (Ahr ϩ/ϩ ). Transcript profiles were determined both in untreated mice and in mice treated 19 h earlier with 1000 g/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Expression of 456 ProbeSets was significantly altered by TCDD in an AHR-dependent manner, including members of the classic AHRE-I gene battery, such as Cyp1a1, Cyp1a2, Cyp1b1, and Nqo1. In the absence of exogenous ligand, AHR status alone affected expression of 392 ProbeSets, suggesting that the AHR has multiple functions in normal physiology. In Ahr Ϫ/Ϫ mice, only 32 ProbeSets exhibited responses to TCDD, indicating that the AHR is required for virtually all transcriptional responses to dioxin exposure in liver. The flavin-containing monooxygenases, Fmo2 and Fmo3, considered previously to be uninducible, were highly induced by TCDD in an AHR-dependent manner. The estrogen receptor ␣ as well as two estrogen-receptor-related genes (␣ and ␥) exhibit AHR-dependent expression, thereby extending cross-talk opportunities between the intensively studied AHR and estrogen receptor pathways. p53 binding sites are over-represented in genes down-regulated by TCDD, suggesting that TCDD inhibits p53 transcriptional activity. Overall, our study identifies a wide range of genes that depend on the AHR, either for constitutive expression or for response to TCDD.Initial studies of the aryl hydrocarbon receptor (AHR) focused on its roles in regulating the induction of CYP1 enzymes (Nebert et al., 2004) and mediating toxicity of dioxinlike chemicals (Okey et al., 2005). More recently, the creation of mice with altered AHR signaling revealed phenotypic changes that implicate the AHR in multiple aspects of growth, development, differentiation, and physiology, irrespective of exposure to toxic environmental chemicals (Fernandez-Salguero et al., 1995;Lahvis et al., 2000;Bunger et al., 2003; Walisser et al., 2004a,b). The AHR is a member of the basic helix-loop-helix PAS superfamily and is located in the cytoplasm in association with chaperone proteins such as heat shock protein 90 and XAP2. The AHR is activated by binding to TCDD, translocates to the nucleus, and dimerizes with another basic helix-loop-helix protein, ARNT. The activated AHR/ARNT heterodimer complex interacts with AHresponsive elements and activates the expression of AHR target genes (Nebert et al., 2004).Mice in which the Ahr gene has been knocked out (Ahr Ϫ/Ϫ ) are extraordinarily resistant to TCDD toxicity (Mimura et al., 1997;Peters et al., 1999;Bunger et al., 2003). Major toxic effects in mice such as hepatic toxicity, thymic atrophy, and cleft palate formation (Bunger et al., 2003) require that the AHR have an intact nuclear translocation/transactiva...