Discovery and comprehension of detailed molecular signaling pathways underlying endothelial vascular morphogenic events including endothelial lumen formation are key steps in understanding their roles during embryonic development, as well as during various disease states. Studies that used in vitro three-dimensional (3D) matrix endothelial cell morphogenic assay models, in conjunction with in vivo studies, have been essential to identifying molecules and explaining their related signaling pathways that regulate endothelial cell morphogenesis. We present methods to study molecular mechanisms controlling EC lumen formation in 3D collagen matrices. In vitro models representing vasculogenesis and angiogenesis, whereby EC lumen formation and tube morphogenesis readily occur, are described. We also detail different methods of gene manipulation in ECs and their application to analyze critical signaling events regulating EC lumen formation.