Pompe disease is a lysosomal storage disorder caused by a deficiency of acid alpha glucosidase (GAA). Diagnosis of Pompe disease is typically based on an enzyme analysis of blood or tissues, such as fibroblasts, followed by confirmation through molecular testing. The advent of fluorometric and mass spectrometry methods for enzyme analysis in dried blood spots (DBS) has simplified the diagnostic approach for Pompe disease, facilitating high-throughput screening of at-risk populations and newborn infants. The following unit will provide the detailed analytical protocol for measurement of GAA activity in DBS using tandem mass spectrometry.