Title: "Stroke Optimization for Microswimmers using the Boundary Element Method" Abstract: Swimming, i.e., being able to advance in a fluid in the absence of external propulsive forces by performing cyclic shape changes, is particularly demanding at low Reynolds numbers. This is the regime of interest for microorganisms and micro- or nano-robots, where hydrodynamics is governed by Stokes equations, and swimming is complicated by the fact that inertial effects are negligible, and viscosity dominates over all participating forces. We reformulate the swimming problem in the context of Control Theory, and show global controllability, as well as some existence results for a general class of microswimmers. For a subset of this class, we present a numerical approximation scheme based on Boundary Element Methods (BEM) and reduced space Successive Quadratic Programming (rSQP) that is capable of computing efficiently optimal strokes for a variety of micro swimmers, both biological and artificial, of which we show some significant examples.