Abstract Cysteine sulfoxides are known for their canceroprotective and antioxidant potential and have been detected in several plants, mainly those belonging to the leek family ( Alliaceae ). A number of these plants are used as herbal remedies, spices, or vegetables, including garlic ( Allium sativum ), onion ( Allium cepa ) and leek ( Allium porrum ). Determination of the quality and pharmacological activity of garlic-containing herbal remedies produced from garlic powder is by measurement of their content of the cysteine sulfoxide alliin. A convenient method allowing reliable routine estimation of the alliin levels present in the fresh plant material through to the final remedy is urgently required. The newly developed flow-through method described in this paper was designed in order to fulfill this demand. In contrast to conventional HPLC methods, neither a pre-column derivatization nor a chromatographic separation are required allowing a high throughput of samples. This technique is based on immobilized alliinase (EC 4.4.1.4), which was combined with an ammonia gas electrode mounted in a miniaturized flow-through cell. The lower detection limit obtained for alliin was 3.7×10 −7 M alliin. High specificity for alliin was demonstrated for the electrode and a variety of garlic samples including garlic powders, dry extracts and garlic tablets were analyzed successfully. Results obtained with the new method showed a good correlation with those obtained with conventional HPLC methods. In conclusion, the flow-through method provides a valuable method for quality control of garlic preparations and screening plant materials for their cysteine sulfoxide-related health potential.