Due to its selectivity and sensitivity, CE coupled to MS (CE-MS) has evolved as a useful analytical tool for determining drugs and metabolites in biological samples. A generic CE-ESI/MS method was developed for the enantioselective determination of basic compounds in plasma. The use of protein precipitation (PP) prior to a hydrodynamic injection (HD) was well adapted to high-concentration samples (>1 ppm) and allowed high throughput. In contrast, the combination of liquid-liquid extraction (LLE) and electrokinetic injection (EK) was time-consuming but did allow detection at the ppb level. Both approaches were fully validated according to ICH guidelines and SFSTP protocols for two pharmaceutical compounds (ecstasy and methadone (MTD)). Deuterated internal standards (IS) in the analytical procedures were used and good quantitative performance was obtained in terms of trueness and precision (repeatability and intermediate precision) since accuracy profiles were within the acceptance limits (30% for biological assay). Methods were linear over the concentration range of 0.50-175 ng/mL and 0.25-5 mug/mL for LLE-EK and PP-HD procedures, respectively. The LLE-EK methodology was finally successfully applied to quantitation of ecstasy and MTD in real cases obtained from toxicology.