We present an integrated 3D virtual environment for the quantitative modeling of the anatomy and the physiology of the pulmonary system. Our approach formally integrates 3D deformable object modeling with conventional models of respiratory mechanics. We demonstrate quantitatively, aspects of the behavior of the respiratory system qualitatively known to clinicians, such as normal quiet breathing and an open sucking chest wound. Our methodology is general and can be used to model both the anatomy and the physiology at many levels of detail. Another important aspect of our approach is that based on our previously developed computer vision techniques we can make such a simulation patient specific. The usefuleness of such a system is manifold. Medical education, surgical planning, disease diagnosis are some of the many areas such a system can be applied.