The refereed proceedings of the Second International Workshop on Functional Imaging and Modeling of the Heart, FIMH 2003, held in Lyon, France in June 2003. The 29 revised full papers presented together with 2 invited papers were carefully reviewed and selected for presentation. The papers are organized in topical sections on anatomy extraction and description, modeling of the cardiac mechanics and functions, electro-physiology and electro- and magnetography, motion estimation, image registration and image analysis, and data acquisition and experimental and modeling issues.