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A detailed model of red blood cell (RBC) transport in a capillary network is an indispensable element of a comprehensive model for the supply of the human organism with oxygen and nutrients. In this paper, we introduce a two-phase model for the perfusion of a capillary network. This model accounts for the special role of RBCs, which have a strong influence on network dynamics. Analytical results and numerical simulations with a discrete model and a generic network topology indicate that there exists a local self-regulation mechanism for the flow rates and a global de-mixing process that leads to an inhomogeneous haematocrit distribution. Based on the results from the discrete model, we formulate an efficient algorithm suitable for computing the pressure and flow field as well as a continuous haematocrit distribution in large capillary networks at steady state.