The dioxin receptor belongs to the basic helix-loop helix/Per-Arnt-Sim (bHLH)/PAS family of proteins and functions as a ligand-dependent transcription factor to activate target genes. The function of the PAS domain of the dioxin receptor is only partially understood. Whereas the C-terminal half of the PAS domain has been shown to harbor ligand binding activity and to function as an accessory dimerization interface, the precise functional role of the N-terminal half of the PAS domain remains unclear. We have previously shown that this domain confers dimerization specificity to the dioxin receptor. Here we report the identification and characterization of a novel nuclear export sequence (NES) motif, located in the N-terminal portion of the PAS domain, in addition to the previously identified NES in the bHLH domain. By point mutagenesis, we have generated a dominant positive form of the PAS domain NES motif that inhibits accumulation of the dioxin receptor in the nuclear compartment of the cell. This mutant form of the receptor was furthermore unable to sustain reporter gene activation. Importantly, we demonstrate that the ligand-free and ligand-occupied forms of the dioxin receptor differentially employ the two NES motifs. In the absence of ligand, nuclear export is sustained via the PAS domain NES, whereas following ligand-dependent activation nuclear export of the receptor is mediated by the NES in the bHLH domain.