Ion migration in electrophoresis always leads to the formation of ionic boundaries. While some types of the ionic boundaries can be formed intentionally, e.g., to improve separation efficiency or sensitivity of the analysis, other, naturally formed boundaries, may cause unexpected effects during the electrophoretic experiment. Some of the boundaries often go unnoticed in practice; however, many effects of the ionic boundaries formed by the sample matrix and background electrolyte components are frequently observed in capillary electrophoresis (CE). The interpretation of these effects may not be trivial and different explanations of the same phenomena may be found in the literature. This critical article attempts to review some of the important effects of the ionic boundaries observed or utilized during the CE of biologically important samples.