Abstract: During a neuro-surgical intervention, the brain tissues shift and warp. In order to keep an accurate positioning of the surgical instruments, one has to estimate this deformation from intra-operative images. 3D ultrasound (US) imaging is an innovative and low-cost modality which appears to be suited for such computer-assisted surgery tools. In this paper, we present a new image-based technique to register intra-operative 3D US with pre-operative Magnetic Resonance (MR) data. A first automatic rigid registration is achieved by the maximisation of a similarity measure that generalises the correlation ratio. Then, brain deformations are tracked in the 3D US time-sequence using a "demon's" like algorithm. Experiments show that a registration accuracy of the MR voxel size is achieved for the rigid part, and a qualitative accuracy of a few millimetres could be obtained for the complete tracking system.