Chelerythrine exhibits pronounced antitumor and apoptosis activities. In order to provide insights into the molecular mechanism of its pharmacological effects, binding selectivity of chelerythrine to a series of single-base bulged DNA hairpins has been assayed by using spectrofluorometric technique. The results indicated that chelerythrine binds specifically to C- and T-bulge sites in DNA hairpins, while sanguinarine exhibits extremely weak binding selectivity to any single-base bulged DNA hairpins, although it has very similar structure with chelerythrine.