The invention provides methods, compositions and kits for enzyme replacement therapy as well as molecular constructs, cells, tissues and plants suitable for expressing recombinant enzymes. Similarly, the invention provides methods for recombinantly producing and orally administering certain metabolic or lysosomal enzymes such as acid alpha glucosidase (GAA) alone, in a pharmaceutical composition or with an activator protein (AGA). Also, the invention provides methods for treating a glycogen storage disease type II (GSDII) or acid maltase deficiency (AMD) or Pompe disease or Fabry disease.