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In the field of angiogenesis research considerable effort is put in the development of in vitro assays of angiogenesis to replace animal experiments. Unfortunately, reproducibility of these assays frequently fails depending on the particular batch of endothelial cells delivered by the distributor. This is due to the lack of reliable markers for the identification and isolation of angiogenic microvascular endothelial cells that have the capacity to perform all stages of the angiogenic cascade. This study was carried out to identify potential markers for angiogenic versus non-angiogenic endothelial cells. The protein expression profile of four capillary-derived human microvascular primary endothelial cell cultures of which only two batches could be stimulated to angiogenesis was investigated and compared by two-dimensional gel electrophoresis. Seven proteins were found to be expressed in the angiogenic batches only. One protein was detected exclusively in the non-angiogenic batches. These proteins might be verified as markers for angiogenic endothelial cells.