The cDNAs for the four murine aryl hydrocarbon (Ah) receptor alleles were cloned and sequenced, and the deduced amino acid sequences were compared. The Ahb-1 allele encodes a protein of 805 amino acids, the Ahd and Ahb-2 alleles encode proteins of 848 amino acids, and the Ahb-3 allele encodes a protein of 883 amino acids. The alleles differ by eight point mutations in the common open reading frame (the initial 805 amino acids) and by additional sequences at the carboxyl end. The amino halves of the proteins, containing a spliced leader sequence, a basic helix-loop-helix motif, and two 50-amino acid repeats (PAAS), have identical sequences except for a single amino acid change in the second PAAS box. The Ahd allele, which has a lower ligand binding affinity, differs from the Ahb-2 receptor by only two amino acids. Mutagenesis experiments with these cloned cDNAs, using in vitro transcription and translation and 2-[125I]iodo-7,8-dibromodibenzo-p-dioxin binding, indicate that the low ligand binding affinity of the Ahd allele is attributable to a valine at residue 375; changing this amino acid to an alanine, as in the Ahb-2 protein, enhances the affinity 4-fold. For in vitro translated Ahb-1 and Ahb-2 alleles the Kd values were approximately 6-10 pM and for Ahd the Kd value was approximately 37 pM. Using 5' truncation and mutations to produce 3' translation truncation sites, we mapped the ligand binding region for the Ahb-1 allele.