In a method of manufacturing a semiconductor device, an isolation region is formed in a substrate, such that the isolation region surrounds an active region of the substrate in plan view. A first dielectric layer is formed over the active region. A mask layer is formed on a gate region of the first dielectric layer. The gate region includes a region where a gate electrode is to be formed. The mask layer covers the gate region, but does not entirely cover the first dielectric layer. The first dielectric layer not covered by the mask layer is removed such that a source-drain region of the active region is exposed. After that, the mask layer is removed. A second dielectric layer is formed so that a gate dielectric layer is formed. The gate electrode is formed over the gate dielectric layer.