We investigate the mechanism of aggregation of red blood cells (RBC) in capillary vessels. We use a discrete-particle model in 3D to model the flow of plasma and RBCs within a capillary tube. This model can accurately capture the scales from 0.001 to 100 microm, far below the scales that can be modeled numerically with classical computational fluid dynamics. The flexible viscoelastic red blood cells and the walls of the elastic vessel are made up of solid particles held together by elastic harmonic forces. The plasma is represented by a system of dissipative fluid particles. Modeling has been carried out using 1 to 3 million solid and fluid particles. We have modeled the flow of cells with vastly different shapes, such as normal and "sickle" cells. The two situations involving a straight capillary and a pipe with a choking point have been considered. The cells can coagulate in spite of the absence of adhesive forces in the model. We conclude that aggregation of red blood cells in capillary vessels can be stimulated by depletion forces and hydrodynamic interactions. The cluster of "sickle" cells formed in the choking point of the capillary efficiently decelerates the flow, while normal cells can pass through. These qualitative results from our first numerical results accord well with the laboratory findings.