High-performance liquid chromatography (HPLC) is a technique most frequently used for the assessment of biologically active peptides. Owing to the ionic character of these compounds, they may also be separated and assayed using capillary electrophoresis (CE), which offers very high efficiency, short analysis time and low consumption of reagents, and is used increasingly more often. The paper describes the combination of HPLC and CE in order to increase the efficiency of the separation of complex mixture of peptides (active substance and its related impurities). The developed two-dimensional HPLC-CE technique was employed for the analysis of the impurities of octreotide, a cyclic octapeptide used in therapy. Because distinct separation mechanisms are used, the two-dimensional technique ensures higher separation efficiency and a more comprehensive impurity profile of the medicinal product than either of the techniques used separately.