Epsilon toxin (epsilon-toxin), produced by Clostridium perfringens types B and D, causes fatal enterotoxaemia in livestock. The disease is principally manifested as severe and often fatal neurological disturbance. Oedema of several organs, including the brain, is also a clinical sign related to microvascular damage. Recombinant epsilon-toxin-green fluorescence protein (epsilon-toxin-GFP) and epsilon-prototoxin-GFP have already been characterised as useful tools to track their distribution in intravenously injected mice, by means of direct fluorescence microscopy detection. The results shown here, using an acutely intoxicated mouse model, strongly suggest that epsilon-toxin-GFP, but not epsilon-prototoxin-GFP, not only causes oedema but is also able to cross the blood-brain barrier and accumulate in brain tissue. In some brain areas, epsilon-toxin-GFP is found bound to glial cells, both astrocytes and microglia. Moreover, cytotoxicity assays, performed with mixed glial primary cultures, demonstrate the cytotoxic effect of epsilon-toxin upon both astrocytes and microglial cells.