Aptamers are oligonucleotides that are isolated and amplified on the basis of their recognition of a target molecule. In this study, an RNA aptamer isolated and amplified on the basis of its affinity for flavin mononucleotide (FMN) was covalently bound to the inner walls of fused-silica capillaries. This aptamer recognizes the flavin moiety of both FMN and flavin adenine dinucleotide (FAD). When an attempt was made to evaluate these capillaries according to existing theory, the theory proved to be insufficient. We describe a new method to evaluate capillaries for use in open-tubular capillary electrochromatography (OTCEC) of charged analytes, which combines OTCEC and flow-counterbalanced capillary electrophoresis. This method enabled us to extract k' and evaluate k(CEC) values for these capillaries, and the dependence of these values on Mg(2+) concentration was explored. The k' values for these capillaries ranged from 0.0951 to 0.2530 and from 0.0255 to 0.1118 for FMN and FAD, respectively.