Cross-reacting material 197 (CRM197), a non-toxin mutant of diphtheria toxin, could act as a diphtheria toxin receptor-specific carrier protein for the targeted delivery of macromolecular substances across the blood-brain barrier (BBB) in vitro. This study was performed to investigate the effects and mechanisms of CRM197 on the permeability of BBB in guinea pigs. Data from the Evans blue extravasation showed that the BBB permeability significantly increased after CRM197 injection in a dose-dependent manner. Transmission electron microscopy indicated CRM197 could induce increased pinocytotic vesicles and vacuoles in brain microvascular endothelial cells. Immunohistochemistry and western blot assay revealed that CRM197 enhanced caveolin-1 protein expression in brain microvessels. The caveolin-1 protein in the membrane fraction of microvessels began to upregulate at 5 min and reached the peak at 10 min after CRM197 treatment, associated by diminished expression of several tight junction-associated proteins ZO-1, occludin, and claudin-5. Thus, our results indicate that the in vivo targeting CRM197 leads to increased BBB permeability via upregulation of caveolin-1 protein, increased pinocytotic vesicles, and redistribution of tight junction-associated proteins in brain microvessels. CRM197 may have a potential application for targeted drug delivery across the BBB.