Nanoparticles (NPs) are increasingly applied in research and development of new therapies. Characterization of NP systems most often include size, shape, size distribution, and charge but information on the chemical stability of NPs and investigation of the presence of dissolved species is most often missing in efficacy studies due to lack of appropriate methods. In this study, a method based on capillary electrophoresis coupled to inductively coupled plasma mass spectrometry (CE-ICP-MS) was established for analysis of selenium (Se) NPs and dissolved Se species in aqueous media. Peak area and migration time precisions (RSD) of 1.4-3.0% and 1.0-2.6%, respectively, were obtained. CE-ICP-MS analysis of a commercially available SeNP suspension (Q-SeNP) revealed large amounts of selenite corresponding to 32% of the total Se content in the suspension, indicating considerable NP degradation upon storage. The CE-ICP-MS method was modified using a coated fused silica capillary in order to analyze SeNPs in human plasma. Peak area and migration time precisions (RSD) in the range of 3.3-10.7% and 0.8-2.8%, respectively, were achieved. Degradation of polyvinyl alcohol (PVA)-coated SeNPs to selenite in human plasma was demonstrated using the modified method. The amounts of SeNP and selenite were estimated based on a correction factor for the ICP-MS signals of PVA-SeNP and dissolved Se. To the best of our knowledge, this is the first study of SeNPs by CE-ICP-MS and highlights the potential of CE-ICP-MS for quantitative characterization of the behavior of SeNPs in biological media.