A three-dimensional nonvolatile memory device comprises a plurality of cell strings arranged perpendicular to a substrate. The nonvolatile memory device is programmed by identifying a selected word line and a plurality of unselected word lines connected to at least one of the cell stings, and sequentially applying a negative voltage and a pass voltage to the selected and unselected word lines, and then applying a program voltage to the selected word line while continuing to apply the pass voltage to the unselected word lines.