Although SDS-PAGE is the method of choice for most denaturing gel electrophoresis procedures, the anionic detergent SDS still presents some drawbacks. For example, SDS forms crystals at low temperatures and, in some cases, causes proteins to aggregate or precipitate. In addition, some proteins are not well-resolved in SDS gels or may migrate anomalously. In these situations, the use of a cationic detergent for PAGE offers an alternative approach. The system described in this protocol uses the cationic detergent cetyltrimethyl ammonium bromide (CTAB) and includes a stacking gel based on the zwitterion arginine (used as a stacking agent) and tricine (N-tris[hydroxymethyl]-methylglycine) used as a counterion and buffer. Some proteins separated on the CTAB electrophoresis system retain their native enzymatic activity, provided the samples are prepared without boiling and without the addition of a reducing agent.