This document discusses the challenges of developing multicompartment drug delivery systems. It outlines three main challenges: 1) defining the architecture so aggregates have distinct containers and self-terminate, 2) enabling defined communication between compartments, and 3) achieving defined encapsulation of drugs. DNA-mediated self-assembly may help address the first challenge of creating well-defined, self-assembled and self-terminated aggregates. Future work is still needed to solve challenges around compartment communication and encapsulation to realize the benefits of multicompartment drug delivery systems.