Integral transforms, such as the Laplace and Fourier transforms, have been major tools in mathematics for at least two centuries. In the last three decades the development of a number of novel ideas in algebraic geometry, category theory, gauge theory, and string theory has been closely related to generalizations of integral transforms of a more geometric character. "Fourier-Mukai and Nahm Transforms in Geometry and Mathematical Physics" examines the algebro-geometric approach (Fourier-Mukai functors) as well as the differential-geometric constructions (Nahm). Also included is a considerable amount of material from existing literature which has not been systematically organized into a monograph. Key features: Basic constructions and definitions are presented in preliminary background chapters - Presentation explores applications and suggests several open questions - Extensive bibliography and index. This self-contained monograph provides an introduction to current research in geometry and mathematical physics and is intended for graduate students and researchers just entering this field.