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Two-dimensional (2D) culture systems do not represent the native microenvironment of the cells which is known to be three dimensional (3D), and surrounded by other cells from all directions. There exist interactions with other cell types in the same vicinity and this also cannot be replicated in a 2D culture. To study the cell-cell interactions between two or more cell types and their biological functions, a few 3D models have been used by different investigators. We have designed a 3D model to investigate the cell-cell interactions between various types of ovarian cells. The same model was also used to study the interactions between prostate cancer epithelial cells and stromal cells. This model uses hydrogel as the anchor matrix to fabricate the constructs and microencapsulation techniques to design multilayered microcapsules. In these multilayer microcapsules the different types of cells are compartmentalized by a sequential encapsulation process. In this chapter, we provide the protocol to compartmentalize two cell types in the same multilayer microcapsules. Although this chapter describes the fabrication of multilayer microcapsules with ovarian cells, the same approach could be applied to other multi-cell tissue-engineered constructs that require cell-cell interactions.