A method of fabricating a three-dimensional semiconductor device is provided. The method includes providing a substrate with a peripheral circuit region and a cell array region; forming a peripheral structure on the peripheral circuit region, and forming an electrode structure on the cell array region. The electrode structure includes a lower electrode, a lower insulating planarized layer on the lower electrode, and upper electrodes and upper insulating layers vertically and alternatingly stacked on the lower insulating planarized layer, and the lower insulating planarized layer may be extended to cover the peripheral structure on the peripheral circuit region. An upper insulating planarized layer is formed to cover the electrode structure and the lower insulating planarized layer on the peripheral circuit region.