Arterial fluid-structure interaction (FSI) computations involve a number of numerical challenges. Because blood flow is incompressible, iterative solution of the fluid mechanics part of the linear equation system at every nonlinear iteration of each time step is one of those challenges, especially for computations over slender domains and in the presence of boundary layer mesh refinement. In this paper we address that challenge. As test cases, we use equation systems from stabilized finite element computation of a bifurcating middle cerebral artery segment with aneurysm, with thin layers of elements near the arterial wall. We show how the preconditioning techniques, we propose for solving these large sparse nonsymmetric systems, perform at different time steps of the computation over a cardiac cycle. We also present a new hybrid parallel sparse linear system solver 'DD-Spike' and demonstrate its scalability. Copyright (C) 2010 John Wiley & Sons, Ltd.