The cellular character of blood leads to complex flow phenomenology in vessels that are of comparable size to that of blood cells. We have designed and implemented an advanced algorithm that simultaneously solves for the dynamics of the highly deformable blood cells and their flow in such confined geometries. It is a boundary integral solver, with fast methods for evaluating the hydrodynamic interactions and spherical harmonics for representing cell shapes. The talk will include an outline of this method and demonstrations for model configurations. It will then be applied for three studies which will be briefly summarized. (1) The first involves the transport of magnetic nanometer-scale particles in small vessels, which can be used for target drug or hyperthermia treatment. Stirring through interaction with the red blood cells lead these to marginate to vessel walls, but this is non-trivially coupled with applied magnetic forces. (2) The second is a study of the flow of red-blood cells through a model spleenic slit, which seems to represent the smallest blood passages in the body. An instability-like bifurcation is identified that is potentially important physiologically and for engineered microdevices that process blood. (3) The talk will finish with an investigation of the hemodynamic forces at play in the nascent circulatory system in early embryonic development. Motivated by specific observations in mouse embryos, we investigate the specific role of red blood cells in the forces that might be sense by the walls of developing vessels.