A simple method for performing continuous elution electrophoresis using a mini-slab-gel system has been developed. The high resolving power of this method provides a means to separate complex mixtures of proteins and recover individual peptides in high yields. Recoveries between 89 and 99% were achieved using a single percentage gel to separate a mixture of standard proteins radiolabeled with 125I. Peptide fragments between 2.5 and 60 kDa generated by CNBr digestion of albumin were isolated within 150 min. Application of continuous elution electrophoresis to the purification of proteins associated with the rat hepatocyte cell adhesion molecule, cell-CAM 105, resulted in complete separation of the two predominant isoforms and the purification of three immunologically unrelated proteins that were coisolated during immunoaffinity chromatography.