In the brain, utrophin is present in the choroid plexus epithelium and vascular endothelial cells, whereas the short C-terminal isoform of dystrophin (Dp71) is localized in the glial end-feet surrounding blood vessels. Both proteins serve as anchors for the so-called dystrophin-associated protein complex (DPC), composed of isoforms of syntrophin, dystroglycan and dystrobrevin. Numerous transporter proteins and channels have a polarized distribution in vascular endothelial cells and in glial end-feet, suggesting an association with the DPC. We investigated the composition and localization of the DPC in dependence on the anchoring proteins in mice lacking either utrophin (utrophin0/0) or dystrophin isoforms (mdx3Cv). Three distinct complexes were identified: (i) associated with utrophin in the basolateral membrane of the choroid plexus epithelium, (ii) associated with utrophin in vascular endothelial cells, and (iii) associated with Dp71 in the glial end-feet. Upon ablation of utrophin or Dp71, the corresponding DPCs were disrupted and no compensation of the missing protein by its homologue was observed. Association of the water channel aquaporin 4 with the glial DPC likewise was disrupted in mdx3Cv mice. These results demonstrate the essential role of utrophin and Dp71 for assembly of the DPC and suggest that these proteins contribute to the proper functioning of the cerebrospinal fluid and blood-brain barriers.