In this work, a zwitterionic molecular micelle, poly-epsilon-sodium-undecanoyl lysinate (poly-epsilon-SUK), was synthesized and employed as a coating in open tubular capillary electrochromatography (OT-CEC) for protein separation. The zwitterionic poly-epsilon-SUK containing both carboxylic acid and amine groups can be either protonated or deprotonated depending on the pH of the background electrolyte; therefore, either an overall positively or negatively charged coating can be achieved. This zwitterionic coating allows protein separations in either normal or reverse polarity mode depending on the pH of the background electrolyte. The protein mixtures contained four basic proteins (lysozyme, cytochrome c, alpha-chymotrypsinogen A, and ribonuclease A) and six acidic proteins (myoglobin, deoxyribonuclease I, beta-lactoglobulin A, beta-lactoglobulin B, alpha-lactalbumin, and albumin). Protein separations were optimized specifically for acidic (reverse mode) and basic (normal mode) pH values. Varying the polymer thickness by changing the polymer and salt concentration had a great influence on protein resolution, while nearly all peaks were also baseline resolved in both modes using the optimized poly-epsilon-SUK coating concentration of 0.4% (w/v). Proteins in human sera were separated under optimized acidic and basic conditions in order to demonstrate the general utility of this coating. Nanoscale characterizations of the poly-epsilon-SUK micellar coatings on silicon surfaces were accomplished using atomic force microscopy (AFM) to gain insight into the morphology and thickness of the zwitterionic coating. The thickness of the polymer coating ranged from 0.9 to 2.4 nm based on local measurements using nanoshaving, an AFM-based method of nanolithography.