This paper describes a micellar electrokinetic chromatography with indirect laser-induced fluorescence detection method for the simultaneous determination of adenine and guanine in DNA extracts from fungus, maize and soybean. The baseline separation was achieved within 2.5min with running buffer (pH 9.3) composed of 10mM borate, 20mM SDS, 3.0x10(-7)M fluorescein sodium as background reagent, applied voltage of 27.5kV, cartridge temperature of 25.0 degrees C. Good linearity relationships (correlation coefficients>0.9917) between the second-order derivative peak heights (RFU) and concentrations of the analytes (mgml(-1)) were obtained. The detection limits in second-order derivative electrophoregrams were 1.16x10(-3)mgml(-1) for adenine and 0.29x10(-3)mgml(-1) for guanine, respectively. The RSD data of intra-day for migration times and second-order derivative peak heights were less than 0.59 and 4.09%, respectively. This developed method was applied to the analysis of the two purines in DNA extracts with recoveries in the range of 85.3-110.2%. In this work, although the detection sensitivity was lower than that of direct LIF, yet the method has the advantages of rapidness and simplicity. And it would also extend the application range of LIF detector.