In a method of manufacturing a semiconductor device, a first gate structure and a second gate structure are formed on a substrate in a first region and a second region, respectively. A first semiconductor pattern including germanium is formed in the first region on the substrate. A first metal layer is formed on the substrate to cover the first semiconductor pattern. A first heat treatment process is performed such that the first semiconductor pattern and the first metal layer react with each other to form a first metal-semiconductor composite pattern in the first region and a semiconductor material of the substrate and the first metal layer react with each other to form a second metal-semiconductor composite pattern in the second region. The first metal-semiconductor composite pattern is removed from the substrate. A second metal layer is formed on the substrate to cover the second metal-semiconductor composite pattern. The second metal layer includes a material different from the first metal layer. A second heat treatment process is performed such that the substrate and the second metal layer react with each other to form a third metal-semiconductor composite pattern.