A capillary electrophoresis method with direct UV detection was developed for the determination of fosmidomycin, a promising new anti-malarial drug, in human serum and urine. Optimization of the separation parameters resulted in a buffer system adjusted to pH 10.8 containing a cationic reagent and an organic modifier. Under these conditions, the migration time of fosmidomycin was 5.2 min with serum and 7.4 min with urine samples. Validation of the method revealed good recoveries, precision and accuracy. The limit of quantification was 0.5 microg/ml in serum and 10 microg/ml in urine. The determination of fosmidomycin in serum was linear over a range of 0.1-150 microg/ml. Short and long-term stability tests resulted in no significant loss of fosmidomycin. The described technique will provide a fast and accurate analytical method for future pharmacokinetic studies.