The paper describes how borate-containing BGEs modify zeta-potential and so EOF in bare fused silica capillaries. This surface modification can be used to suppress EOF and improve the separation performance of CZE including capillary sieving electrophoresis (CSE). Boric acid forms complexes with polysaccharides used as sieving matrices in CSE and other compounds containing hydroxyl groups, including polyol bases such as Tris, triethanolamine, and Bis-Tris propane. High concentration of boric acid in BGEs leads to a strong interaction of boric acid with the silica surface of the capillary wall and this suppresses or even completely eliminates zeta-potential and EOF. Using a polyol base with several charge-carrying amino groups, such as Bis-Tris propane, can actually reverse EOF. We demonstrate the use of various borate-containing BGEs in bare fused silica capillaries for size-separation of DNA fragments, size-separation of proteins by SDS CSE, and also by CZE in the absence of any sieving matrix.