A new analytical method for the determination of cinchona alkaloids by flow-injection sampling and chemiluminescence (CL) detection is developed. A weak CL can be emitted by oxidation reaction of cinchona alkaloid with potassium permanganate. The conditions for CL emission were investigated and optimized. The linear range of 1.0 × 10−7 – 8.0 × 10−5 g mL−1 was obtained for quinine, quinidine and cinchonine. The detection limit was 3.2 × 10−8 g mL−1 for quinine and 3.0 × 10−8 g mL−1 for quinidine and cinchonine. The recoveries of the three drugs from urine and serum samples were in the range of 95.0–105% with RSDs of 1.7–2.0%. The proposed method was used for the determination of cinchona alkaloids in pharmaceuticals and biological fluids with satisfactory result. The possible CL mechanism is also discussed.