A series of genistein derivatives, prepared by alkylation and difluoromethylation, were tested for their inhibitory effects on the hydrogen peroxide induced impairment in human umbilical vein endothelial (HUVE-12) cells in vitro. The HUVE-12 cells were pretreated with either the vehicle solvent (DMSO), genistein, or different amounts of the genistein derivatives for 30 min before exposed to 1 mM hydrogen peroxide for 24 h. Cell apoptosis was determined by flow cytometry with propidium iodide (PI) staining. Cellular injury was estimated by measuring the lactate dehydrogenase (LDH) release. Data suggested that the genistein derivatives possessed a protective effect on HUVE-12 cells from hydrogen peroxide induced apoptosis and reduced LDH release. Among these derivatives, 7-difluoromethyl-5,4'-dimethoxygenistein exhibited the strongest activity against hydrogen peroxide induced apoptosis of HUVE-12 cells.