Biological fluids drugs analysis are important to investigate the pharmacokinetic and pharmacodynamic of the subministered compounds for the comprehension of their behaviour and bioavailability. Many pharmaceutical preparations contain a chiral molecule as active compound often as racemic mixture of the two enantiomers of which only one exhibits pharmacological effect, the other enantiomer being inactive or responsible of toxicological effects. In fact two enantiomers with almost identical physical and chemical properties can exhibit a different behaviour in an highly stereoselective environment as the human body. With respect to the analytical methods in use for chiral separation Capillary Electrophoresis shows high efficiency and resolution together with feasibility, low costs and very short analysis time. CE and MEKC have been used for enantiomers resolution of antihypertensive and anticoagulant drugs in body fluids. By cyclodextrin modified MECK the separation of mephenytoin and 4-hydroxymephenytoin metabolite in urine samples has been performed in order to identify different phenotypes in the oxidative metabolising ability in man.