The use of an ideal high quality biomaterial with the inherent properties of biocompatibility is the most crucial factor that governs the long term efficiency of this technology. An ideal biomaterial for cell encapsulation should be one that is totally biocompatible, does not trigger an immune response in the host and does not interfere with cell homeostasis so as to ensure high cell viability. However, one major limitation has been the inability to reproduce the different biomaterials and the requirements to obtain a better understanding of the chemistry and biofunctionality of the biomaterials and the microencapsulation system.  Several studies demonstrate that surface modification of these cell containing microparticles allows control over the growth and cellular differentiation. of the encapsulated cells.
One study proposed the use of zeta potential which measures the electric charge of the microcapsule as a means to predict the interfacial reaction between microcapsule and the surrounding tissue and in turn the biocompatibility of the delivery system.