The literature review reveals current analytical methodologies used for pharmaceutical analysis, their advantages and disadvantages. In this context the potential of capillary electrophoresis (CE) is established through a study of the current literature. Capillary electrophoresis method is developed and optimised for alkylxanthines. The achieved separation for these analytes stands out for its high efficiency and especially short analysis time. This work also verifies the potential of CE in the analysis of significant impurities in montelukast sodium - an active ingredient for treatment of bronchial asthma. The obtained method surpasses a chromatographic method currently employed in the pharmaceutical industry in terms of efficiency and time of analysis. Along with the method development this work shows the capability of CE as a fundamental research tool. The determination of the association constants of steroid hormones with cyclodextrins is successfully achieved from the electrophoretic mobilities. A range of different types of natural and derivatised cyclodextrins is investigated. This straightforward approach marks the first time CE has been used for the assessment of steroid/cyclodextrin interaction. For the first time the versatility of CE is demonstrated in the separation of different types of anticancer drugs - anthracyclines and taxanes. The high hydrophobicity of the drugs requires detailed investigation of suitable buffer composition with additives of miscellaneous component and organic phase. The use of these drugs in combination therapy sparked the interest in this application and this study shows the potential of CE for such a challenge. To demonstrate the potential an attempt is made to apply the developed electrophoretic methods to the analysis of plasma samples.