The object of this study was to describe a method of measuring targeting accuracy in functional neurosurgery using MR imaging and the Stereotactic Atlas of the Human Thalamus and Basal Ganglia. This method should be useful for any functional procedure using these tools or similar ones, and is described here in the specific context of focused ultrasound surgery. The authors describe the atlas coordinate system used, the different relevant targeting and accuracy definitions, the tools used, the intraoperative target determination, the postoperative target reconstructions, and the calculation of the therapeutic lesion volume. The proposed method has been applied to the specific situation of measuring targeting accuracy in focused ultrasound functional neurosurgery. The authors found mean absolute global targeting accuracies between 0.54 and 0.72 mm (SDs between 0.34 and 0.42 mm), with 85% of measured coordinates within 1 mm. The proposed method may be particularly useful in the context of functional neurosurgical procedures implying therapeutic ablations, be they through radiofrequency, focused ultrasound, or any other technique. This method allows an ongoing control of the targeting precision, a basic requirement in any functional neurosurgical procedure.