A technique has been developed for automated detection of the intercommissural (AC-PC) line for positron emission tomography (PET). The AC-PC line is estimated from the location of four internal landmarks; the frontal and occipital poles, the inferior aspect of the anterior corpus callosum, and the subthalamic point. The landmarks are detected automatically in PET mid-sagittal slices by combining edge detection, interpolation and profile curve analysis techniques. The anatomical relationships between the true and estimated AC-PC lines from the landmarks was confirmed by analysis of magnetic resonance (MR) images. Accuracy of the automated estimation technique was assessed in co-registered PET and MR images, which showed minimal angular differences and displacements of the estimated from the true AC-PC lines. The automated detection of the AC-PC line in a PET study enables accurate stereotactic localization of functional signals without the need for additional anatomical imaging and provides a basis for objective and reproducible intersubject comparison.