An object is to provide an SOI substrate provided with a semiconductor layer which can be used practically even when a glass substrate is used as a base substrate. Another object is to provide a semiconductor device having high reliability using such an SOI substrate. An altered layer is formed on at least one surface of a glass substrate used as a base substrate of an SOI substrate to form the SOI substrate. The altered layer is formed on at least the one surface of the glass substrate by cleaning the glass substrate with solution including hydrochloric acid, sulfuric acid or nitric acid. The altered layer has a higher proportion of silicon oxide in its composition and a lower density than the glass substrate.