The ability of DNA aptamers to separate nontarget compounds is demonstrated. Two G-quarter forming aptamers, a 15-mer and a 20-mer, were covalently linked to fused silica capillary columns to serve as stationary-phase reagents in capillary electrochromatography. Separations of binary mixtures of amino acids (D-trp and D-tyr), enantiomers (D-trp and L-trp), and polycyclic aromatic hydrocarbons were achieved. Aptamers offer several attractive features for stationary-phase reagents, including ease of synthesis and of attachment to surfaces and modification of their binding properties through minor changes in sequence.