Major behavioral and neurochemical features observed between inbred C57BL/6 and DBA/2 mouse strains can be reproduced within rodent strains following dietary-induced reductions in brain docosahexaenoic acid (DHA, 22:6n-3) composition. It was therefore hypothesized that C57BL/6 and DBA/2 mice exhibit constitutive differences in brain DHA composition that are independent of diet. To test this, adult C57BL/6J and DBA/2J prefrontal cortex, hippocampus, ventral striatum, and midbrain fatty acid composition was determined by gas chromatography. After correction for multiple comparisons, C57BL/6J mice exhibited significantly lower DHA composition in the hippocampus and ventral striatum, but not prefrontal cortex or midbrain, and significantly greater regional arachidonic acid (ARA, 20:4n-6):DHA ratios, relative to DBA/2J mice. C57BL/6J mice also exhibited significantly lower regional adrenic acid (ADA, 22:4n-6) composition, and a significantly smaller ADA:ARA ratio, relative to DBA/2J mice. C57BL/6J mice exhibited significantly smaller oleic acid:stearic acid ratio in the hippocampus and ventral striatum relative to DBA/2J mice. Among all mice, DHA composition was positively correlated with the ADA:ARA ratio and inversely correlated with the oleic acid:stearic acid ratio. These data demonstrate that inbred C57BL/6J and DBA/2J mouse strains exhibit constitutive and region-specific differences in fatty acid composition independent of diet, and suggest that heritable genetic factors are an important determinant of central fatty acid composition.