A gas chromatography-mass spectrometry (GC-MS) method is described for the quantification of guanidinoacetate in different body fluids, using a two step derivatisation procedure which involves a reaction with hexafluoroacetylacetone to form a bis(trifluoromethyl)pyrimidine ring structure followed by a reaction with pentafluorobenzyl bromide. 13C2-labelled guanidinoacetate is used as an internal standard. Bis(trifluoromethyl)pyrimidine pentafluorobenzyl derivatives were separated on a polar capillary GC-column and were quantified using negative chemical ionisation mass fragmentography. The detection limit of the method is 1 pmol guanidinoacetate in a 100 microl sample. Control values were obtained for urine (53.9 +/- 25.9 mmol mol(-1) creatinine), plasma (1.08 +/- 0.31 micromol l(-1)), cerebrospinal fluid (CSF) (0.114 +/- 0.068 micromol l(-1)) and amniotic fluid (3.44 +/- 0.64 micromol l(-1)). The applicability of the method is illustrated by the determination of guanidinoacetate in urine, plasma and CSF of a patient affected with guanidinoacetate methyltransferase deficiency. In all body fluids of this patient, guanidinoacetate was highly elevated.