In this thesis the possibilities of using capillary electrophoresis as a separation technique for analysis of proteins and microbubbles is presented. A complete analytical process consists of five necessary steps of which one is the actual analysis step. For this step a suitable analytical technique is needed. Capillary electrophoresis (CE) is one of the common analytical separation techniques used for analysis of a diversity of analytes, and can be both used in routine analysis and for research purposes. The reason for using CE, compared to other liquid-based separation techniques, is mainly short analysis time, high resolution, and negligible sample volumes and solvent waste. Depending on the characteristics of the analytes, and the sample matrix, different modes of CE can be used, where capillary zone electrophoresis (CZE) is the most employed one. The basic principle of CZE is separation of the analytes due to differences in total mobility, which is dependent on the charge and size of the analytes, and the electroosmotic flow (EOF). The EOF can be controlled by several parameters e.g. choice of background electrolyte (BGE), and the optimization of the parameters has been discussed throughout the thesis. To improve the properties of the BGE, an ethylammonium nitrate (EAN) water solution was used as BGE for CE analysis in Paper I. The precision of the EOF with this method was determined by adjusting the pH of the BGE, the concentration of EAN in the BGE, and the electric field. Model proteins were thereafter analysed using the optimal parameters yielding a precision sufficient for routine control. One example of the applications of CE is separation of novel contrast agents, which consist of polyvinyl alcohol microbubbles (PVA-MBs). In Paper II, a method for analysis of PVA-MBs in biological samples using CE with UV-detection was developed. It was also established that intact PVA-MBs could be distinguished from ultrasound degraded PVA-MBs in the same set-up. / <p>QC 20171012</p>