A method of obtaining a three-dimensional deformation of an organ which is deformable over time and extends in a three-dimensional space from at least two sets of data (DS(t1), DS(t2)) representing points of said organ and corresponding to distinct times (t1, t2) in the deformation of the organ. A correspondence (SEL(t1,t2)) between the points in the sets of data being determined (COR), said method uses a definition (DEF) of notional planes (Pi) on which there are defined explicit equations (EQi) of the deformation of the organ including unknown parameters (PARi(t1, t2)). The parameters (PARi(t1, t2)) are calculated (CAL) for each equation (EQi) and the explicit equations (Esp.) obtained are then utilized (EXT) in order to define the deformation in the three-dimensional space (DEF3D(t1,t2)) by weighting functions defined for the points in the space.