Summary In this paper, we describe a general methodology for the realistic reconstruction and animation of anatomic organs. In fact, in the scope of conformal radiotherapy and hadron therapy applications, we want to simulate the motion and the shape alteration of the internal anatomical objects and to input this knowledge to treatment planning. For the reconstruction, particle systems are used: firstly, surface shape of the considered organ is computed from a set of CT scan sections. Next, the volume defined by this surface is filled with particles. The coherency of the object is maintained due to the use of the classical Lennard-Jones inter particles force. This work permits to study the impact of the organs movement on the treatment of prostate and lung cancer. Our particle system has been suitably integrated in a radiation dose evaluation software, developed within an European BIOMED2 project and is currently supported by the French ETOILE project.