A new flow injection analysis (FIA) system equipped with an electrochemiluminescent (ECL) detector has been developed and applied for the ECL detection of 2-thiouracil. The FIA-ECL system used a specially designed flow-through ECL thin-layer cell to reduce the dead volume, the IR drop across the cell, and the probability of accumulation of gas bubbles in the cell. It was thus envisioned to improve the detection limit of the FIA-ECL method. After being established, the new FIA-ECL system was used to investigate the ECL response of 2-thiouracil in the presence of the ECL of Ru(bpy)3(2+). It was found that 2-thiouracil could enhance the ECL of Ru(bpy)3(2+) over a wide pH range (pH 4.0-12.0). A highly sensitive method for detection of 2-thiouracil in biological samples was developed by the new FIA-ECL system after optimizing several experimental conditions, such as the applied potential of the working electrode, the pH value of the aqueous solution, the flow rate of carrier solution, and the concentration of Ru(bpy)3(2+).