The potential of cell therapy for the regeneration of diseased and damaged tissues is now widely recognized. As a consequence there is a demand for the development of novel systems that can deliver cells to a particular location, maintaining viability, and then degrade at a predictable rate to release the cells into the surrounding tissues. Hydrogels have attracted much attention in this area, as the hydrogel structure provides an environment that is akin to that of the extracellular matrix. One widely investigated hydrogel is alginate, which has been used for cell encapsulation for more than 30 years. Alginate gels have the potential to be used as 3D cell culture systems and as prosthetic materials, both are applied to regeneration of the cornea. Here, we describe an alginate-based process that has been used for encapsulation of mammalian cells including corneal cells, with high levels of viability, and which allows subsequent retrieval of cell cultures for further characterization.