As the pharmaceutical industry continues the daunting search for novel drug candidates, there remains a need for rapid screening methods not only for biological activity, but for physiochemical properties as well. It is invaluable that adequate model systems for absorption and/or bioavailability be developed early in the drug evaluation process to avoid the loss of promising compounds late in development. The focus of this paper is the use of vesicle EKC (VEKC) as a high-throughput, easy, cost-effective, and predictive model for the passive transcellular diffusion of drug candidates in the intestinal epithelium. Vesicles are large aggregates of molecules containing a spherical bilayer structure encapsulating an internal cavity of solvent. It is this bilayer structure that makes vesicles attractive as model membranes. In this study, vesicles were synthesized from both phospholipids and surfactant aggregates, and then employed as pseudostationary phases in EKC (VEKC). The interaction of drug molecules with vesicles in EKC was then used as the basis for an in vitro assay to evaluate passive diffusion. The VEKC technique showed a statistical correlation between the retention of drug candidates using surfactant and phospholipid vesicles and passive diffusion data (log Pow and colon adenocarcinoma). VEKC analysis offers high-throughput capabilities due to the short run times, low sample, and solvent volumes necessary, as well as instrument automation. However, due to the complexity of drug absorption in the intestine, difficulty arises when a single in vitro model is used to predict in vivo absorption characteristics. Therefore, the retention of drug candidates using VEKC in conjunction with other permeability prediction methods can provide a primary screen for a large number of drug candidates early in the drug discovery process with minimal resources.