In this paper, the separation of fifteen plant auxins by capillary electrophoresis was investigated. A simple and efficient method was developed. The migration behaviour of the auxins under different separation conditions was studied. Optimum separation was obtained with cyclodextrin-modified borate-phosphate buffer. This method was applied to the determination of indole acetic acid (1AA), a well known auxin in plant samples, with cinnamic acid as the internal standard. The method is linear over the range of 0.4–8.0 mg/mL, with 82.4% recovery and a limit of quantitation of 0.4 mg/mL.