Neovascularization and invasion are key features of malignant gliomas. Matrix metalloproteinases (MMPs) are supposed to play a major role mediating these processes. To analyze the expression patterns of MMPs in microvascular human cerebral endothelial cells (HCEC), we isolated endothelial cells from normal human brain microvessels. Characterization of cellular origin was performed by immunostaining, using the endothelial cell markers Ulex europaeus Agglutinin-1, von-Willebrand-Factor and Glucose-transporter-1. Contamination by other cell types was tracked by immunohistochemistry for GFAP (astrocytes), ASM (pericytes) and CD68 (macrophages). Secretion of MMPs was evaluated by ELISA and zymography. To determine whether HCEC show any difference in MMP expression compared to endothelial cells of other origin we analyzed human umbilical vein endothelial cells (HUVEC). HCEC show a decrease of MMP-3 and MMP-2 protein when treated with SU5416, a VEGF-R2 (KDR/flk-1) inhibitor, whereas MMP expression remained unchanged in HUVEC. To determine whether these findings show any effect in the motility of these cells we used a three-dimensional co-culture assay of avascular glioblastoma spheroids with primary HCEC spheroids. Untreated controls showed invasion of both cell populations into each other whereas treatment of the co-cultures with SU5416 resulted in complete inhibition of endothelial cell invasion hence indicating that flk-1 related motility of endothelial cells is critically involved in this process and can be studied with this assay. The results of different effects of anti-angiogenic treatment on proteolytic properties of two endothelial cell populations suggest that neovascularization of human brain tumors in vitro is dependent on the surrounding endothelial cell type and should therefore be studied with organ-specific human microvascular cerebral endothelial cells.