Gangliosides have long been implicated in multiple pathologies affecting the central nervous system. Empirical studies have suggested the possibility that gangliosides, particularly GD3, work in tandem with pro-inflammatory cytokines, especially tumor necrosis factor alpha (TNFα), to initiate or facilitate cell death in the CNS. As a step toward unraveling the metabolic pathways activated in the pathogenesis of brain cell death, we have surveyed gene expression for a host of cytokines and chemokines in primary brain cell cultures exposed to GD3, GD1b, and TNFα for 24 h. An initial screen of 98 genes on a focused mini-array revealed the expression of at least 28 genes related to cell growth, death, or inflammation in our system of mixed cells cultured from neonatal rat brains. Clear evidence of a differential response to the gangliosides or TNFα was seen in 12 genes. Quantitative PCR was used to validate the response of six of these genes. We found that both GD3 and GD1b, but not TNFα, up-regulated expression of macrophage inflammatory protein 3 (MIP3A) and interleukin-1 receptor 1 (IL1R1), but down-regulated fibroblast growth factor 13 (FGF13). The expression of FGF receptor activating protein 1 (FRAG1) and interleukin-3 receptor alpha (IL3RA) was down-regulated by GD3. Exposure to TNFα resulted in a dramatic up-regulation of IL3RA and chemokine ligand 2 (CCL2), both of which have been implicated in multiple sclerosis. Our results provide strong evidence that the expression of these genes might be critical links in the metabolic cascades leading to cell degeneration and death in the brain.