The aim of this work was to study the effects of both chemical and instrumental parameters on the separation of beta-agonists (clenbuterol (CLE), salbutamol (SAL) and terbutaline (TER)) by non-aqueous capillary electrophoresis (NACE) method. Due to the number of parameters involved and their interactions, factorial experimental designs (EDs) at two levels was applied to investigate the influence of experimental factors (ionic strength of the background electrolyte (BGE), organic solvent, injection time, voltage and temperature) in sets of several CE responses (resolution, (RS), number of theoretical plate (N), tailing factor (TF) and migration time (tm)). As a compromise between the four responses, the optimum condition was obtained in 18 mM ammonium acetate in methanol (MeOH):acetonitrile (ACN):glacial acetic acid (66:33:1%, v/v/v) using an injection time of 4 s, the voltage and the temperature of 28 kV and 24 degrees C, respectively. The proposed NACE permitted the baseline separation of the three beta-agonists within 10.5 min with good repeatability (%RSD < 3.5%) and linearity (r2 > 0.99). The developed method was applicable for the analysis of the beta-agonists in syrup and tablets and the NACE condition was compatible with a mass spectrometer detector.