A micellar electrokinetic chromatography method is proposed for the determination of morphine, codeine, and paclitaxel at clinical relevant levels in human serum and plasma, which are employed in the treatment of patients with cancer. Optimal conditions for the separation were investigated. A background electrolyte solutions consisting of 20 mM borate buffer adjusted to pH 8.5, sodium dodecyl sulphate 60 mM and 15% methanol, hydrodynamic injection, and 25 kV as separation voltage were used. Detection wavelength was 212 nm for morphine and codeine and 200 nm for paclitaxel. Aspects such as stability of the solutions, linearity, accuracy, precision, and robust and ruggedness were examined in order to validate the proposed method. Detection limits obtained for all the studied compounds ranged between 26 and 52 ng/mL. Before micellar electrokinetic chromatography determination, the samples were purified and enriched by means of an extraction–preconcentration step with a preconditioned C18 cartridge. This method was applied to the analysis of serum and plasma samples from different cancer patients undergoing treatment with paclitaxel or/and codeine.