This work mainly deals with application of the capillary electrophoresis (CE) for determination and separation of physiologically active compounds. The principal determinant of methodology choice, mainly in the field of pharmaceutical industry as well as for any clinical purposes, is speed and simplicity of analysis. Thus, preferred approaches include automated methods with high sensitivity and specificity, which is characteristic for CE. Simply, the motto: ?time is money? rules. Capillary electrophoresis was found to be useful as a verification and confirmation tool in the screening analysis for amphetamines, opiates, benzodiazepines, cocaine and their metabolites for toxicological applications. The other thesis chapter is focused on the determination of drugs belonged to the antiandrogen class (nilutamide and flutamide), employing the micellar electrokinetic chromatography (MEKC). The proposed method allowed their quick separation by addition of sodium dodecyl sulfate to the BGE. Moreover including of on-line preconcentration step to the analytical procedure enabled the determination of drug therapeutic level in serum. The next electrophoretic approach describes antidiabetic drugs determination (rosiglitazone and metformin) using the hyphenation of CE with mass spectrometry (MS). The utilization of the method is applied on the patient serum. Generally, CE is a very promising tool for clinical analysis at the present time and it could be a simple and time saving alternative technique to HPLC and GC. The selectivity of CE can be also utilized for separation of complicated mixtures of target analytes from matrix without multistep sample preparation.