Lesions of the nigrostriatal pathway are known to induce a compensatory up-regulation of various neurotrophic factors. In this study we examined protein content of basic fibroblast growth factor (FGF-2) in tissue samples taken from the ventral midbrain and striatum at two different time points following a neurotoxic lesion of the nigrostriatal pathway in two different rat strains, the outbred Sprague-Dawley (SD) and inbred F344 9 Brown Norway F1 hybrid (F344BNF1). Despite both rat strains having comparable lesions of the nigrostriatal pathway, we observed a difference in the temporal up-regulation of FGF-2 in ventral midbrain samples taken from the side ipsilateral to the lesion. Basic FGF was significantly upregulated in ventral midbrain in SD rats 1 week post-lesion while we did not observe an up-regulation of FGF-2 in the lesioned ventral midbrain of F344BNF1 at this same time point. However, both strains showed a significant up-regulation of FGF-2 in the lesioned ventral midbrain 3 weeks post-lesion. Sprague-Dawley rats also appeared to be more sensitive to the lesion in terms of up-regulating FGF-2 expression. The differences reported here suggest currently unknown genetic differences between these two strains may be important factors for regulating the compensatory release of neurotrophic factors, such as FGF-2, in response to a neurotoxic lesion of the nigrostriatal pathway.