The aryl hydrocarbon nuclear translocator (Arnt) is a basic helix-loop-helix (per/Arnt/Ahr/sim) PAS-containing protein that can heterodimerize with the aryl hydrocarbon receptor (AhR), the hypoxia-inducible factor-1 alpha, and other PAS-containing proteins to form transcriptionally active complexes. To identify the genes whose expression is modulated by Arnt, we used the technique of differential display to compare the expression of genes in wild-type and Arnt-defective (BPRc1) mouse hepatoma (Hepa1c1c7) cells. Here we report two gene products whose expression was reduced in BPRc1 cells (a WW domain-binding, protein-like factor and one unknown gene product) when compared to wild-type cells, and two that were elevated (Steel factor and a serpin-like protein). Comparison of the relative expression of these gene products between two independently-derived, Arnt-defective cell lines, as well as in BPRc1 cells in which Arnt expression was restored by a stably integrated Arnt-expression plasmid, revealed that each gene was expressed in an Arnt-independent manner. Our results clearly demonstrate that gene expression in the variant cell clones is distinctly different from that of the parental wild-type Hepa1c1c7 cells from which they were derived and involves genes in addition to, and unrelated to, that of Arnt. The identification of these differentially expressed gene products suggests that caution should be exercised when using these variant cell lines to confirm the role of the AhR/Arnt-signaling pathway in a given cellular response.