CD133 is a marker for a population of glioblastoma (GBM) and normal neural stem cells (NNSC). We aimed to reveal whether the migratory potential and differentiation of these stem cells is associated with CD133 expression and with cathepsin proteases (Cats). The study confirms CD133 as a prognostic marker for the survival of GBM patients. We demonstrated that normal neural stem cells as well as differentiated malignant GBM cells have higher invasion potential and invade the collagen matrix in a mode different from that of CD133+ GBM stem cell spheres. These results could have implications for the design of new therapeutics, including protease inhibitors.