The separation of nine furanonaphthoquinones by micellar electrokinetic chromatography (MEKC) is described. The running electrolytes used in this method were 0.03 M sodium dodecyl sulphate (SDS) in 0.09 M borate buffer (pH 9) containing 10% methanol, with an applied voltage of 20 kV. Application of this technique in the determination of the main furanonaphthoquinones, 5-hydroxy-2-(1-hydroxyethyl)naphtho[2,3-b]furan-4,9-dione, 8-hydroxy-2-(1-hydroxyethyl)naphtho[2,3-b]furan-4,9-dione, and 2-(1-hydroxyethyl)naphtho[2,3-b]furan-4,9-dione, of Tabebuia impetiginosa is demonstrated in this paper.