The theme of this review is to highlight the importance of microscale electrophoretic-based separation systems in microdialysis (μD). The ability of CE and MCE to yield very rapid and highly efficient separations using just nanolitre volumes of microdialysate samples will also be discussed. Recent advances in this area will be highlighted, by illustration of some exciting new applications while the need for further innovation will be covered. The first section briefly introduces the concept of μD sampling coupled with electrophoresis-based separation and the inherent advantages of this approach. The following section highlights some specific applications of CE separations in the detection of important biomarkers such as low-molecular-weight neurotransmitters, amino acids, and other molecules that are frequently encountered in μD. Various detection modes in CE are outlined and some of the advantages and drawbacks thereof are discussed. The last section introduces the concepts of micro-total analysis systems and the coupling of MCE and μD. Some of the latest innovations will be illustrated. The concluding section reflects on the future of this important chemical alliance between μD and CE/MCE.