A sensitive and specific method was developed for the determination of codeine and morphine in human serum and for the determination of trace amounts of endogenous morphine in human urine. The analytes were recovered from serum by a simple liquid-liquid extraction method. Urine samples were hydrolyzed, and purified by two liquid-liquid extraction steps and a solid-phase extraction. Samples were derivatized to the pentafluoropropionic esters and measured by gas chromatography tandem mass spectrometry. Using the deuterated analogues as internal standards a limit of quantification of 20 fmol/ml (5.7 pg/ml) morphine and 500 fmol/ml (150 pg/ml) codeine in human serum and of 2.5 fmol/ml (0.71 pg/ml) morphine in urine was achieved. The method was suitable for the determination of morphine and codeine in pharmacokinetic studies and for the determination of the urinary excretion of endogenous morphine.