A tetraglucose oligomer, Glcalpha1-6Glcalpha1-4Glcalpha1-4Glc, designated Glc4, has been shown to be a putative biomarker for the diagnosis of Pompe disease. The purpose of this study was to assess whether Glc4 could be used to monitor the therapeutic response to recombinant human acid alpha glucosidase (rhGAA) enzyme replacement therapy (ERT) in patients with Pompe disease. Urinary Glc4 levels in 11 patients receiving rhGAA therapy was determined by both HPLC-UV and stable isotope dilution ESI-MS/MS. Combined Glc4 and maltotetraose, Glcalpha1-4Glcalpha1-4Glcalpha1-4Glc, (M4) concentrations, designated Hex4, in plasma from these patients were measured by HPLC-UV only. Baseline urinary Glc4 and plasma Hex4 in these patients (mean+/-SD: 34.2+/-11.3 mmol/mol creatinine and 1.7+/-0.8 microM, respectively) were higher than age-matched control values (mean+/-SD, 6.1+/-5.1 mmol/mol creatinine and 0.22+/-0.15 microM, respectively). Both urinary Glc4 and plasma Hex4 levels decreased after initiation of ERT for all patients. In the four patients with the best overall clinical response in both skeletal and cardiac muscle, levels decreased to within, or near, normal levels during the first year of treatment. In contrast, levels fluctuated and were persistently elevated above the control ranges in those patients with a less favorable clinical response (good cardiac response but limited motor improvement). These results suggest that urinary Glc4 and plasma Hex4 could serve as a valuable adjunct to clinical endpoints for monitoring the efficacy of therapeutic interventions such as rhGAA ERT in Pompe disease.