Polyelectrolyte microcapsules are made by layer-by-layer (LbL) coating of a sacrificial template, followed by decomposition of the template, to produce hollow microcapsules. In this paper, we report on the in vivo cellular uptake, degradation and biocompatibility of polyelectrolyte microcapsules produced from alternating dextran sulphate and poly-L-arginine layers on a template of calcium carbonate microparticles. We show that a moderate tissue reaction is observed after subcutaneous injection of polyelectrolyte microcapsules in mice. Within sixteen days after subcutaneous injection, most of the microcapsules are internalized by the cells and start to get degraded. The number of polyelectrolyte layers determines the stability of the microcapsules after cellular uptake.