Perhexiline, a chiral drug, is a potent antiischemic agent whose clinical utility is limited by hepatic and neural toxicities. It inhibits mitochondrial carnitine palmitoyltransferase‐1, however, excessive inhibition predisposes toward tissue steatosis. This pilot study investigated the distribution of the two enantiomers and their toxicological potential. Dark Agouti rats (n = 4 per group) were administered vehicle or 200 mg/kg daily of racemic, (+)− or (−)‐perhexiline maleate orally for 8 weeks. Plasma biochemical liver function tests and Von Frey assessments of peripheral neural function were performed. Hepatic and neuronal histology, including lipid and glycogen content, was assessed using electron microscopy. Concentrations of the perhexiline enantiomers and metabolites were quantified in plasma, liver and heart. Plasma perhexiline concentrations following administration of racemate, (+)− or (‐)‐enantiomer were within the mid‐upper clinical therapeutic range. There was extensive uptake of both enantiomers into liver and heart, with 2.5‐ to 4.5‐fold greater net uptake of (+)‐ compared to (−)‐perhexiline (P < .05) when administered as pure enantiomers, but not when administered as racemate. There was no biochemical or gross histological evidence of hepatotoxicity. However, livers of animals administered (+)‐perhexiline had higher lipid (P < .01) and lower glycogen (P < .05) content, compared to those administered (−)‐perhexiline. Animals administered racemic perhexiline had reduced peripheral neural function (P < .05) compared to controls or animals administered (−)‐perhexiline. For the same plasma concentrations, differences in tissue distribution may contribute to disparities in the effects of (+)‐ and (−)‐perhexiline on hepatic histology and neural function.