Benzalkonium chloride (BAC) is a mixture of alkyl substituted benzyl dimethylammonium chloride homologs (C12-BAC, C14-BAC and C16-BAC). Chlorhexidine acetate is a widely used effective component in compound chemical disinfectants. A method for the simultaneous determination of chlorhexidine acetate and benzalkonium chloride in compound chemical disinfectants by capillary electrophoresis (CE) was established. The CE analysis was carried out using an uncoated capillary with 50 microm i. d. and 37 cm total length. The running buffer was 150 mmol/L NaH2PO4-62.5 mmol/L H3PO4 (pH 2.5) containing 40% (v/v) acetonitrile. The sample medium was 50 mmol/L acetic acid-acetonitrile (1:1, v/v). The detection wavelength was 214 nm. The factors such as the buffer concentration and pH, the content of acetonitrile, which influenced the separation and accurate assay of compound chemical disinfectants were investigated in detail. The intra-day and inter-day precisions of the method were below 3. 0% and 3.7%, respectively. The limits of detection (LOD, signal to noise ratio (S/N) = 3) for chlorhexidine acetate, C12-BAC, Cl4-BAC and C16-BAC were 0. 3, 0.5, 0.5 and 0.5 mg/L, respectively. The limits of quantification (LOQ, S/N = 10) were 1.0, 1.5, 1.5, and 1.5 mg/L, respectively. The corrected peak area and the mass concentration of the four components mentioned above showed good linear relationships within the ranges of 1.0 - 400 mg/L, 1. 5 - 200 mg/L, 1.5 - 200 mg/L and 1.5 - 200 mg/L, with linear correlation coefficients (r) of 0.9995, 0.9998, 0.999 7 and 0.9998, respectively. The established method was used for the determination of the four disinfectants in the compound chemical disinfectants. The results were in good agreement with those obtained by the high performance liquid chromatographic method.