We describe a microchip capillary electrophoresis method for the analysis of nitrate and sulfate in ambient aerosols. Investigating the chemical composition of ambient aerosol particles is essential for understanding their sources and effects. Significant progress has been made towards developing mass spectrometry-based instrumentation for rapid qualitative analysis of aerosols. Alternative methods for rapid quantification of selected high abundance compounds are needed to augment the capacity for widespread routine analysis. Such methods could provide much higher temporal and spatial resolution than can be achieved currently. Inorganic anions comprise a large percentage of particulate mass, with nitrate and sulfate among the most abundant species. While ion chromatography has proven very useful for analyzing extracts of time-integrated ambient aerosol samples collected on filters and for semi-continuous, on-line particle composition measurements, there is a growing need for development of new compact, inexpensive approaches to routine on-line aerosol ion analysis for deployment in spatially dense, atmospheric measurement networks. Microchip capillary electrophoresis provides the necessary speed and portability to address this need. In this report, on-column contact conductivity detection is used with hydrodynamic injection to create a simple microchip instrument for analysis of nitrate and sulfate. On-column contact conductivity detection was achieved using a Pd decoupler placed upstream from the working electrodes. Microchips containing two Au or Pd working electrodes showed a good linear range (5-500 microM) and low limits-of-detection for sulfate and nitrate, with Au providing the lowest detection limits (1 microM) for both ions. The completed microchip system was used to analyze ambient aerosol filter samples. Nitrate and sulfate concentrations measured by the microchip matched the concentrations measured by ion chromatography.