The present invention provides a pharmaceutical composition comprising a protein having α-galactosidase activity for treating Fabry disease, which causes no allergic side effect, which is highly stable in blood (plasma) and which can readily be taken up by a cell of an affected organ. The pharmaceutical composition for treating Fabry disease of the invention comprises, for example, a protein which acquires an α-galactosidase activity through alteration of the structure of the active site of wild-type human α-N-acetylgalactosaminidase.
