We tested the hypothesis that exercise-induced changes in hippocampal brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) differ among rat strains exhibiting a range of voluntary wheel running activity. Four strains (Sprague-Dawley, Brown Norway, Dark Agouti and PVG) were given access to running wheels (1 or 7 nights). Over 7 nights, the average distance run per night was higher in PVG versus other strains, and higher in Brown Norway versus Sprague-Dawley rats. Hippocampal BDNF concentrations in sedentary rats were higher in PVG versus Sprague-Dawley rats. When data from all strains were combined, BDNF levels increased with 7 nights of wheel running and were positively correlated to the previous night distance run. Sedentary hippocampal NT-3 levels were not different between rat strains, but decreased with 7 nights of wheel access; NT-3 was negatively correlated with previous night distance run. There were no differences between strains in the correlation between distance run and BDNF or NT-3 levels. Although exercise decreases hippocampal NT-3, strain does not alter NT-3 levels. In contrast, BDNF levels increase with exercise and basal levels differ between strains, possibly due to strain differences in spontaneous activity.