Inclusion Criteria: * Male or female subjects 18 to 50-years old * Have a diagnosis of Pompe disease, as defined by protein assay AND/OR DNA sequence of the acid alpha-glucosidase gene, AND clinical symptoms of the disease * Have residual ability to complete the 10 meter walk test * Willing to discontinue aspirin, aspirin-containing products and other drugs that may alter platelet function, 7 days prior to dosing, resuming 24 hours after the dose has been administered * Consistently taking enzyme replacement therapy (ERT) or remain off ERT from baseline until Day 520 * United States residents only. Exclusion Criteria: * Be pregnant or nursing, and if the subject is of child bearing potential they should use contraception until the end of the study * Have required oral or systemic corticosteroids within the last 15 days prior to baseline screening * Have a platelet count less than 75,000/mm\^3 * Have an INR greater than 1.3 * Have seronegative to AAV9 capsid protein (neutralizing Ab titers \<1:5 and total binding Ab titer \<50 U/ml) * Have transaminases and alkaline phosphatase more than ten times the upper limit of normal at screening or Day-1 * Have bilirubin and gamma-glutamyl transpeptidase greater than 2 times the upper limit of normal at screening or Day -1 * Have any chronic liver disease (aside from hepatic dysfunction related to Pompe disease) such as hepatitis B and C and cirrhosis * Be currently, or within the past 30 days, participating in any other research protocol involving investigational agents or therapies * Have history of platelet dysfunction, evidence of abnormal platelet function at screening, or history of recent use of drugs that may alter platelet function, which the subject is unable/unwilling to discontinue for study agent administration * Have received gene transfer agents within the past 6 months * Have any medical condition or circumstance for which an MRI evaluation is contraindicated * Have any other concurrent condition that, in the opinion of the investigator, would make the subject unsuitable for the study * Inconsistent with use of ERT.