Intestinal bacteria have been shown to be important in regulating drug metabolism of the host. However, little is known about the effect of exogenous bacteria, such as probiotic-treatment and conventionalization of germ-free conditions on the host hepatic drug-metabolizing enzymes and potential adverse “bug-drug” interactions. VSL#3 is a potent probiotic-combination that is clinically used for irritable bowel syndrome and ulcerative colitis. The purpose of this study was to quantify the expression of approximately 90 critical drug-metabolizing enzymes in livers of conventional and germ-free mice treated with or without VSL#3 (in drinking water for 4-weeks), as well as in livers of conventionalized (2-month) germ-free mice. Bacterial 16S rRNA qPCR in the large intestinal content confirmed the colonization of certain VSL#3 components. In liver, the cytochrome P450 (Cyp) 3a gene cluster, which encodes the major xenobiotic-metabolizing enzymes, as well as the Cyp4a and 4f gene clusters, which encode the lipid-metabolizing enzymes, were examined. RT-qPCR demonstrated that VSL#3 had minimal effects on the Cyp3a and 4a mRNAs; however, it increased the mRNAs of Cyp4f37 and Cyp4v3 in conventional mice. Germ-free condition decreased the mRNAs of Cyp3a11, 3a25, 3a41a/b, and 3a44, whereas conventionalization partially restored their expression. In contrast, germ-free condition increased the mRNAs of Cyp4a10, 4a14, 4a31, and 4a32, whereas conventionalization reduced their expression to conventional levels. Western blot confirmed that VSL#3 had no effect on Cyp3a11 or 4a14 proteins, whereas conventionalization restored the conventional levels of Cyp3a11 and further decreased Cyp4a14 protein. In conclusion, short-term VSL#3 has minor effects on the expression of hepatic drug-metabolizing enzymes; germ-free conditions markedly decreased the Cyp3a but increased the Cyp4a gene expression, whereas conventionalization normalizes the expression of these enzymes.