Although single artificial vesicles are successfully used as delivery vehicles of pharmaceuticals, unilamellarity and restriction to one vessel result in premature content release in physiological environments as well as problems in simultaneous entrapment of a given set of (pharmaceutical) components. Multilamellarity and assemblies of distinct populations of vesicles are proposed to solve these problems. In this study, we provide a novel encapsulation protocol to fabricate multilamellar vesicles and we report on the DNA-mediated self-assembly of more than two distinct populations of vesicles. We discuss how these results might be used in personalized healthcare based on custom-tailored encapsulated multicompartment vesicular drug delivery systems.