A sequential injection analysis (SIA) system is described for the simultaneous determination of L-and D-carnitine using amperometric biosensors as detectors. The SIA system was used, because of its high precision, accuracy and low sample and buffer consumption. The biosensors were designed using physical and chemical immobilization of L-amino acid oxidase and horseradish peroxidase (HRP) for the assay of L- carnitine, and D-amino acid oxidase and HRP for the assay of D-carnitine. The linear concentration ranges are in the pmol/l to nmol/l magnitude order, with very low limits of detection. The biosensors/SIA system was used reliably for on-line process control of the enantiopurity of carnitine with a frequency of 34 samples per hour.