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Abstract: We present the design, setup and results for a magnetic navigation system for small animal stereotactic neurosurgery. Our system tracks the position of thin (diameter 0.5 mm), magnetized ferromagnetic probes inserted into brains of small animals, e.g. rats, for electrophysiological recordings. It is used in combination with the spherical assistant for stereotactic surgery (SASSU) robot to obtain online feedback of the probe\'s position. Navigation is based only on the static magnetic field generated by the probes thus no external excitation or wires are needed. The magnetic field created by the probe is measured by three sensors and compared to data of a previously generated lookup table. To account for overlaying magnetic fields (e.g earth\'s field), we determine and adjust for the magnetic background. A nearest neighbor approach is used to identify the best element of the lookup table. The actual position of the probe is found using trilinear interpolation between the best element and its neighbors. To validate the system, the workspace was filled with gelatin to simulate brain\-like, organic structure. Next, several positions were approached by the robot. The difference between the ground truth position and the position determined by the system was calculated. We found that the norm of the mean values are between 0.09 mm and 0.64 mm with a norm of the standard deviation between 0.52 mm and 0.80 mm. No substantial difference between gelatin and non\-gelatin data was observed. Our approach allows the online validation of the probe\'s position in X\-,Y and Z\-axis. We conclude that accurate localization of small ferromagnetic objects is feasible with our system. Currently, we are working on further applications including the use in human surgery, e.g. dermatology