A method is developed for the determination of substituted methoxy phenols and aromatic acids in biomass burning aerosol using capillary electrophoresis (CE) coupled to an electrospray ionization mass spectrometer. Background electrolytes (BGEs) containing ammonium acetate, ammonium hydroxide and 10% (v/v) methanol at pH 9.1 and ammonium hydroxide at pH 11 are investigated for their suitability. A good linearity is found for all analytes in the range of 1-50 microM for the ammonium acetate based BGE and 1-40 microM for the ammonium hydroxide BGE. The detection limit ranged from 0.1 to 1.0 microM for the ammonium acetate based BGE and 0.3 to 0.7 microM for the ammonium hydroxide BGE. The relative standard deviation (R.S.D.) is typically less than 0.5% (ammonium acetate based BGE) and 4.2% (ammonium hydroxide BGE) for the migration time and 3-9% (ammonium acetate based BGE) and 2.5-8% (ammonium hydroxide BGE) for the peak area (n = 5). The analytical time was less than 10 min for both methods. The proposed methods are fast, sensitive and quantitative and can be applied to the analysis of complex biomass burning aerosol samples without complex pre-treatment. The results from the analysis of real biomass burning samples demonstrate the suitability of the proposed methods to the analysis of low concentration water soluble organic carbon (WSOC) in biomass burning samples. The fast analytical time and high sensitivity of the proposed methods enables the analysis of a large number of size segregated impactor samples from biomass burning aerosols.