A simple nonaqueous capillary electrophoresis method is described for the separation of several atropine and scopolamine related drugs. The analysis of these pharmaceutical compounds was performed in a methanol-acetonitrile (25/5, v/v) mixture containing 25 mM ammonium acetate and 1 M acetic acid. The robustness was proved using a full factorial design at two levels. The method was validated and successfully applied for the determination of N-butylscopolamine in different pharmaceutical preparations. Results were compared to those obtained by a capillary electrophoresis method based on aqueous media.