Abstract: The invention provides recombinant native lysosomal enzymes produced by liver cells, preferably in vitro, and methods of using the native recombinant lysosomal enzymes to treat enzyme deficiencies in vivo. Lysosomal enzymes, including acid alpha-glucosidase (GAA), produced by liver cells apparently undergo the post-translational modifications necessary to achieve good enzymatic activity. The resulting enzymes can be taken up by various other cells and can correct phenotypic abnormalities of distant organs with enzyme deficiencies. In certain preferred embodiments, the enzyme is GAA and the methods are especially adapted for treatment of type II glycogen storage disease in mammals, including humans.