In this study, borate is shown to be key in the high-performance capillary electrophoretic (HPCE) separation of several biologically-active molecules differing only by a single hydroxyl group with no change in net charge. Separation of several paired compounds is minimal or nonexistent in 100 mM tricine buffer at pH 8.4, while identical analysis with 100 mM borate buffer led to baseline resolution in less than 10 min, most likely due to complexation of borate with the molecules containing a cis-diol. In contrast, baseline separation of tyrosine from the cis-diol-containing compounds dopa and dopamine is achieved with either buffer system because of differences In their charge due to the p-hydroxyl group of the benzene ring. The equilibrium complexation of borate with cytidine can be monitored by HPCE through a borate concentration-dependent change in the borate-cytidine complex migration time (MT). A semilogarithmic plot of the change in MT versus borate concentration suggests an equilibrium dissociation constant for the complex of 15 mM, a value consistent with literature values for borate-ribose complex formation.