It has been reported that the severe cerebral edema produced in experimental animals by Clostridium perfringens (Cl p) type D ε toxin can be prevented by prior treatment with its precursor prototoxin due to competitive binding to endothelial cells (ECs) at the blood–brain barrier (BBB). In this study we investigate the effects of the prototoxin on the BBB, without added toxin. The integrity of the BBB was assessed by its ability to prevent leakage of endogenous albumin. ECs at the BBB were studied by immunocytochemistry for any alteration in the endothelial barrier antigen (EBA), a molecular marker for the intact BBB. Immunocytochemistry showed rapid but mild opening of the BBB to endogenous albumin. Light and electron immunocytochemistry showed qualitative and quantitative reduction in EBA immunoreactivity, with a spectrum of changes at time intervals from 1 h to 14 days post-prototoxin injection. Some vessels with ultrastructural changes and widening of the perivascular space retained EBA immunoreactivity. Many vessels showed partial or complete loss of EBA staining with minimal widening of the perivascular space and edema. Recovery of EBA expression was still incomplete at 14 days postinjection. This is the first report to show endothelial cell damage, mild reversible cerebral edema, and alteration in BBB markers following administration of Cl p prototoxin. This model of mild brain edema may be useful for BBB studies.