The field of nanoscience is expected to make significant contributions to contemporary medicine by providing unique solutions to critical problems. These solutions require the design of hybrid materials/systems with new properties and functionalities. This review focuses on spherical polymer nanocompartments (capsules and vesicles) and describes their potential in a wide variety of medical applications that range from passive drug carriers to active nanoreactors to artificial organelles. Here, we place emphasis on the complex requirements that a polymer assembly must fulfill for consideration in the medical domain. In terms of stability and chemical diversity, synthetic polymer compartments are superior to currently marketed liposomes, thereby supporting their modification for targeting approaches, stimuli-responsiveness, and multifunctionality. The authors present the latest concepts and examples based on the encapsulation/entrapment of biomolecules (e.g., enzymes and proteins) for the development of active nanosystems for application in the medical domain.