We established an analytical methodology for guanidinoacetate and creatine determination by gas chromatography-mass spectrometry with the use of stable isotopes as internal standards. The method showed good precision and high sensitivity, and it requires minimal sample handling. We determined the reference values in urine and plasma. In urine both guanidinoacetate concentration and creatine/creatinine ratio decrease as age increases, but no significant differences were found in plasma. In addition, 15 patients with urea cycle defects were analysed and showed low guanidinoacetate concentrations when compared with age-matched controls. We concluded that guanidinoacetate concentration is a parameter to be considered in the follow-up of patients with urea cycle defects, and arginine should be supplemented in sufficient amounts, as the brain seems to be impermeable to creatine influx, but not to its precursor, arginine, which is needed for creatine, protein, and NO synthesis.