The AHR locus encodes the aryl hydrocarbon receptor (AHR), a transcriptional regulator of multiple drug-metabolizing enzymes and mediator of toxicity of dioxin-like chemicals. The Han/Wistar (Kuopio) rat strain (H/W) is remarkably resistant to lethal effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) because of a point mutation in the exon/intron 10 boundary in AHR genomic structure that leads to use of 3 alternative cryptic splice sites, potentially creating 3 alternative transcripts and 2 protein products. The deletion variant (DV), which lacks 43 amino acids in the transactivation domain, has the highest intrinsic transactivation activity in vitro; amino acids 766 to 783 suppress transactivation function. However, DV expression levels in H/W rats in vivo are low in liver, lung, thymus, kidney, and testis; insertion variant mRNAs (IVs) are the dominant mRNA forms in H/W rats in which wild-type AHR mRNA is undetectable. In dioxin-sensitive rat strains and lines that are homozygous for wild-type AHR alleles, wild-type AHR mRNA is the most abundant transcript but some IV transcripts are detectable. TCDD treatment in vivo increases transcript levels for both the DV and IVs in H/W rats and increases wild-type transcript levels in dioxin-sensitive rats but does not alter which transcript forms are expressed. In silico modeling indicates that the DV mRNA has lost considerable secondary structure, whereas at the protein level, the transactivation domain of the IV in the dioxin-resistant H/W rat has greater alpha-helical content and a more hydrophobic terminus than wild-type AHR, which may produce a protein conformation that is less amenable to interaction with other regulatory proteins.