This volume is a collection of articles by speakers at the conference ""Poisson 2006: Poisson Geometry in Mathematics and Physics"", which was held June 5-9, 2006, in Tokyo, Japan. Poisson 2006 was the fifth in a series of international conferences on Poisson geometry that are held once every two years. The aim of these conferences is to bring together mathematicians and mathematical physicists who work in diverse areas but have common interests in Poisson geometry. The program for Poisson 2006 was remarkable for the overlap of topics that included deformation quantization, generalized complex structures, differentiable stacks, normal forms, and group-valued moment maps and reduction. The articles represent current research in Poisson geometry and should be valuable to anyone interested in Poisson geometry, symplectic geometry, and mathematical physics. This volume also contains lectures by the principal speakers of the three-day school held at Keio University that preceded Poisson 2006.