This paper presents realistic computer simulation of deformation of the brain subject to in-vivo indentation. The work presented provides a step towards neurosurgical simulation, with applications to non-rigid registration, virtual reality training and operation planning systems and robotic devices to perform minimally invasive brain surgery. In order to properly analyze experimental data collected in-vivo, a three-dimensional, non-linear finite element model of the brain was developed. Magnetic resonance imaging techniques were used to obtain geometric information needed for the model. The shape of the force-displacement curve obtained using the numerical solution was very similar to the experimental one. The predicted forces were about 31% lower than those recorded during the experiment. Having in mind that the coefficients in the model had been identified based on experimental data obtained in-vitro, and large variability of mechanical properties of biological tissues, such agreement can be considered as very good. By appropriately increasing material parameters describing instantaneous stiffness of the tissue one is able, without changing the structure of the model, to reproduce experimental curve almost perfectly. Numerical studies showed also, that the linear, viscoelastic model of brain tissue is not appropriate for the modeling brain tissue deformation even for moderate strains.