The process of gastrulation is an important early stage of morphogenesis. It is a very complex procedure, during which the organs of the foetus take their initial shape. It is controled by genetic, chemical and mechanical factors, but the contribution of each one of them to the procedure, is still unknown. Invagination is the initial step of gastrulation. During this procedure, the cells are guided by chemotaxy, in order to supply their energy demand. It has been observed that some cells start to take the shape of a bottle (bottle-cells), decreasing their surface close to the nourishment fluid. As a result of their surface reduction, the neighboring cells are pulled toward the bottle cells. This results to the blastula performing an inner folding and finally “surrounding” the nourishment. The movement of cells during gastrulation is gravely affected by the centriole, the cadherins and the myosin fibers. They are inner-cell structures composed by proteins. The understanding of the effect of these factors on cell beavior, is a crucial step towards explaining the entire procedure of morphogenesis. We propose in this article an approach of the phenomenon of invagination based exclusively on the laws of physics and mechanics. For this purpose, we have created a three-dimensional model and attempted to simulate the initiation of the procedure of invagination. The results of our experiments show that in-vivo cell behavior is adequately simulated and that this approach can be enhanced in order to simulate other genetic processes as well.