This book constitutes the proceedings of the Second 3D Physiological Human Workshop, 3DPH 2009, held in Zermatt, Switzerland, in November/December 2009. The 19 revised full papers presented were carefully reviewed and selected from numerous submissions. The papers are organized in topical sections on Segmentation, Anatomical and Physiological Modelling, Simulation Models, Motion Analysis, Medical Visualization and Interaction, as well as Medical Ontology.