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In this paper, we present a multimodal registration method applied to gated positron emission tomography (PET), X-ray Computed Tomography (CT) and Magnetic Resonance (MR) cardiac images. CT images acquired on the same device as the PET ones are used as link to merge anatomical MR images and functional PET images. The registration process is divided in two steps: a 3D structure registration and a grey-levels registration. This approach enables global to local transformations. The structure registration uses a 3D biventricular heart model initialized on CT and MR data to define a rigid transform. This global registration is then refined with a grey-levels step based on mutual information and free form deformations. To improve endocardium registration, we propose a composite PET-CT image to find the optimal transformation on MR image. We also take into account the temporal problematic of heart motion by initializing the searched transformation, at a current frame, with the composition of a monomodal transformation (representing the heart motion between the previous and current frames) and a multimodal one (representing the spatial transformation between the two images at the previous frame).