Fumonisin B1 (FB1) is mycotoxin produced by Fusarium verticillioides (formerly F. moniliforme), a fungal contaminant of corn and other cereals found worldwide. Fumonisin B1 causes number of diseases in farm animals including the species-specific disorder, equine leukoencephalomalacia (ELEM). FB1 inhibits ceramide synthase and as a consequence disrupts metabolism of sphingolipids. Deregulation of sphingolipid metabolism results in accumulation of free sphingoid bases, activation of cytokine expression and depletion of complex sphingolipids. We hypothesized that lack of neurotoxic effects in species other than equine following systemic administration of FB1 is due to the restricted availability of this mycotoxin in the brain. The pre-exposure to the lipopolysaccharide (LPS) resulted in the disruption of blood brain barrier (BBB). When mice were treated concurrently with FB1 an accumulation of sphinganine, a biomarker for FB1 availability to the tissue, was observed in brain. The combined administration of LPS and FB1 caused modulation of proinflammatory cytokines in brain and liver after repeated FB1 treatment. These results indicate that sphingolipid metabolism in the adult brain is vulnerable to the exposure of FB1 when accompanied by the endotoxin-related damage to the BBB. The intracerebroventricular (icv) infusion of FB1 led to the neuronal degeneration in cortex. The icv treatment caused regional accumulation of free sphingoid bases but sphingomyelin and complex sphingolipids were not depleted. Potent FB1-induced activation of proinflammatory signaling was observed in cortex. These results show that adult murine brain is vulnerable to the direct exposure of FB1 when the protective BBB barrier is bypassed. FB1 induced necrotic cell death in both BV-2 and primary astrocytes and exhibited potent antiproliferative properties toward the BV-2 cells. Neuronal cells were relatively resistant to the toxic effects of FB1. In all cells the FB1 treatment disrupted the sphingolipid metabolism, as indicated by the accumulation of free sphinganine and decrease of free sphingosine. These findings indicate that glial cells, namely microglia and astrocytes, may be a primary targets in the FB1-induced neurotoxicity.