Groupoids often occur when there is symmetry of a nature not expressible in terms of groups. Other uses of groupoids can involve something of a dynamical nature. Indeed, some of the main examples come from group actions. It should also be noted that in many situations where groupoids have been used, the main emphasis has not been on symmetry or dynamics issues. For example, a foliation is an equivalence relation and has another groupoid associated with it, called the holonomy groupoid. While the implicit symmetry and dynamics are relevant, the groupoid records mostly the structure of the space of leaves and the holonomy.More generally, the use of groupoids is very much related to various notions of orbit equivalence. The point of view that groupoids describe 'singular spaces' can be found in the work of A. Grothendieck and is prevalent in the non-commutative geometry of A. Connes. This book presents the proceedings from the Joint Summer Research Conference on 'Groupoids in Analysis, Geometry, and Physics' held in Boulder, CO. The book begins with an introduction to ways in which groupoids allow a more comprehensive view of symmetry than is seen via groups. Topics range from foliations, pseudo-differential operators, $KK$-theory, amenability, Fell bundles, and index theory to quantization of Poisson manifolds. Readers will find examples of important tools for working with groupoids. This book is geared to students and researchers. It is intended to improve their understanding of groupoids and to encourage them to look further while learning about the tools used.