The arithmetic motivic Poincare series of a variety $V$ defined over a field of characteristic zero, is an invariant of singularities which was introduced by Denef and Loeser by analogy with the Serre-Oesterle series in arithmetic geometry. They proved that this motivic series has a rational form which specializes to the Serre-Oesterle series when $V$ is defined over the integers. This invariant, which is known explicitly for a few classes of singularities, remains quite mysterious. In this paper we study this motivic series when $V$ is an affine toric variety. We obtain a formula for the rational form of this series in terms of the Newton polyhedra of the ideals of sums of combinations associated to the minimal system of generators of the semigroup of the toric variety. In particular, we deduce explicitly a finite set of candidate poles for this invariant.