Genz-123346 is a potent and selective glucosylceramide synthase (GCS) inhibitor that blocks the conversion of ceramide to GL1. It has been studied as a potential treatment of diabetes mellitus, polycystic kidney disease and fatty liver disease. Genz-123346 improved glucose tolerance and increased insulin sensitivity in two animal models of type 2 diabetes. In Zucker diabetic fatty rats, treatment with Genz-123346 significantly lowered blood glucose levels and partially prevented the normal deterioration of pancreatic β-cell function over time and preserved the ability of the islets to secrete insulin. In the high-fat–fed diet-induced obese mice, Genz-123346 essentially normalized A1C levels to that of the lean animals. Inhibiting GSL synthesis ameliorates the liver pathology associated with obesity and diabetes in mice model. Blockade of kidney glucosylceramide GlcCer accumulation with the GCS inhibitor Genz-123346 effectively inhibits cystogenesis in mouse models orthologous to human autosomal dominant polycystic kidney disease (PKD) (Pkd1 conditional knockout mice) and nephronophthisis (jck and pcy mice). Molecular analysis in vitro and in vivo indicated that inhibition of GCS by Genz-123346 inhibited the AKT-mTOR signaling pathway. It induced autophagy via the AKT-mTOR signaling pathway in HEK293T cells, increased autophagy flux and reduced mutant α-syn levels in mouse primary neurons potentially via indendent mechanisms. Exposure of cells to Genz-123346 and to other GCS inhibitors at non-toxic concentrations can enhance the killing of tumor cells by cytotoxic anti-cancer agents. This chemosensitizing activity was unrelated to lowering intracellular glycosphingolipid levels. Genz-123346 is a substrate for multi-drug resistance efflux pumps such as P-gp (ABCB1, gP-170). In cell lines selected to over-express P-gp or which endogenously express P-gp, chemosensitization by Genz-123346 was primarily due to the effects on P-gp function. Genz-123346 has little effect on 1-O-acylceramide synthase activity at concentrations that effectively inhibit GL1 synthase activity and therefore do not significantly elevate cell ceramide levels in vitro. Unlike N-butyldeoxynojirimycin (NB-DNJ), another inhibitor of GCS Genz-123346 does not inhibit α-glucosidase or glucocerebrosidase.