BACKGROUND: The C57BL/6 mouse model has been used extensively in alcohol drinking studies, yet significant differences in ethanol preference between substrains exist. Differences in ethanol-induced dopamine release in the ventral striatum could contribute to this variability in drinking behavior as dopamine has been implicated in the reinforcing properties of ethanol. METHODS: A 2-bottle choice experiment investigated the difference in ethanol preference between C57BL/6J and C57BL/6NCrl animals. Microdialysis was used to determine dopamine release and ethanol clearance in these 2 substrains after intraperitoneal injections of 1.0, 2.0 and 3.0 g/kg ethanol or saline. RESULTS: C57BL/6J mice exhibited significantly greater ethanol preference and less ethanol-stimulated dopamine release compared with C57BL/6NCrl mice. The intraperitoneal injections of ethanol caused a significant increase in dopamine in both substrains at all 3 doses with significant differences between substrains at the 2 highest alcohol doses. Saline injections had a significant effect on dopamine release when given in a volume equivalent to the 3 g/kg ethanol dose. Ethanol pharmacokinetics were similar in the 2 substrains at all 3 doses. CONCLUSIONS: Ethanol-induced dopamine release in the ventral striatum may contribute to the differences in alcohol preference between C57BL/6J and C57BL/6NCrl mice.