Contrast agents are widely used to enhance the image quality in clinical imaging using e.g. ultrasound. The contrast agents used for ultrasound imaging are mainly microbubbles (MBs) with a soft or hard shell encapsulating a core of gas. In the present study, MBs with a hard shell of polyvinyl alcohol (PVA), and a core of air were analysed in a capillary electrophoretic system using a UV area imaging detector. The detector was operating at 3 wavelengths; 214 nm, 255 nm and 525 nm, and the highest absorbance for individual PVA-MBs were obtained at 214 nm. Two detection windows and a vertical loop capillary position enabled tracking of the PVA-MBs both in an upward and a downward flow direction, where PVA-MBs had different flow distributions and slightly higher average flow velocity upwards, attributed to temperature differences in the capillary that was part within the instrument and part outside. The tracking also allowed counting and quantification of the PVA-MBs. Separation of PVA-MBs from proteins present in human blood plasma was achieved, with multi-wavelength imaging showing best contrast at 525 nm. The PVA-MBs absolute values of negative zeta potential and anionic mobility when injected from plasma in the pH 12 background electrolyte are higher than those obtained for MBs injected from buffer, consistent with their increased negative charge due to a protein corona coating of the PVA-MBs.