Patients with glycogen storage disease type II (GSD II) typically excrete increased amounts of a glycogen-derived glucose tetrasaccharide, Glcalpha1-6Glcalpha1-4Glcalpha1-4Glc (Glc(4)), in the urine. With the advent of a new enzyme replacement therapy for GSD II, there is a need for early identification of patients with this disease and for monitoring the efficacy of treatment. Glc(4) is a good candidate biomarker for GSD II. A simple and robust method using stable isotope dilution-electrospray ionization-tandem mass spectrometry for the analysis of Glc(4) in biological samples was developed. A 13C(6)-labeled stable isotope internal standard was synthesized by transglycosylation using a recombinant alpha-amylase. Butyl 4-aminobenzoate derivatives of Glc(4) and the internal standard were analyzed using multiple reaction monitoring. This method was shown to be accurate and precise by the repeated analysis of calibrators and quality control samples in urine and plasma. There was good agreement with a high-performance liquid chromatography-UV method for urine samples, whereas there was less agreement with plasma samples. Accurate determination from dried urine spot samples was also demonstrated. This method is amenable to high-throughput analysis, a necessary prerequisite for mass screening for GSD II.