This book constitutes the thoroughly refereed post-conference proceedings of the Third International Workshop on Statistical Atlases and Computational Models of the Heart: Imaging and Modelling Challenges, STACOM 2012, held in conjunction with MICCAI 2012, in Nice, France, in October 2012. The 42 revised full papers were carefully reviewed and selected from numerous submissions. The papers are organized in topical sections on CFD challenge, DE-MRI segmentation challenge, LV landmark detection challenge, motion tracking analysis challenge, and regular papers.