Capillary electrophoresis (CE) is a well-established and frequently used technique in the pharmaceutical industry. Therefore an appropriate analytical instrument qualification (AIQ) is required for quality assurance. AIQ forms the basis of a quality management followed by analytical method validation, system suitability tests (SSTs) and quality control checks. Two parts of the AIQ, namely the operational qualification (OQ) and the performance qualification (PQ) are of particular interest in the daily routine of the laboratory. A new concept for OQ and PQ was developed to assure the correct function of a CE system. The significance of each parameter, possible test methods as well as acceptance criteria will be presented and discussed in detail. Especially temperature adjustment by the cooling system and the voltage supply must be tested for accurate and precise operation. The detector noise, wavelength accuracy and detector linearity have to be checked as well. Finally, the injection linearity, accuracy and precision need to be qualified. The proposed set of qualification procedures is easy to implement and was already tested on five CE instruments from three different manufacturers. A time- and cost-saving continuous PQ was derived, using results from method-specific SSTs and some additional experiments. This holistic concept continuously surveys the most relevant parameters, hence assuring the suitability of the used instruments and decreasing their downtimes.