The nearly tissue equivalent MRI properties and the unique ability of registering 3D dose distributions of polymer gels were exploited to assess the total geometrical accuracy in clinical Gamma Knife applications, taking into account the combined effect of the unit’s mechanical accuracy, dose delivery precision and the geometrical distortions inherent in MR images used for irradiation planning. Comparison between planned and experimental data suggests that the MR-related distortions due to susceptibility effects dominate the total clinical geometrical accuracy which was found within 1 mm. The dosimetric effect of the observed sub-millimetre uncertainties on single shot GK irradiation plans was assessed using the target percentage coverage criterion, and a considerable target dose underestimation was found.