Provided are three-dimensional semiconductor devices and methods of operating the same. The three-dimensional semiconductor devices may include active patterns arranged on a substrate to have a multi-layered and multi-column structure and drain patterns connected to respective columns of the active patterns. The methods may include a layer-selection step connecting a selected one of layers of the active patterns selectively to the drain patterns. For example, the layer-selection step may be performed in such a way that widths of depletion regions to be formed in end-portions of the active patterns are differently controlled depending on to a height from the substrate.