Introduction In gamma knife (GK) radiosurgery, target and organs at risk (OARs) delineation is performed directly in MR images after they have been registered to the Leksell coordinate system (LCS). This registration can be performed either using the fiducial markers generated in the MR images by the N-shaped rods on the Leksell MR localization or through anatomical-based co-registration to corresponding registered (using the fiducial markers) CT images. Purpose To compare the two different methods used in GK radiosurgery for MR image registration and assess geometric differences and differences induced in plan quality and DVH-indices clinically used for plan evaluation and acceptance. Materials and methods A plan cohort formed by 20 patients with acoustic neuroma and pituitary adenoma treated using GK radiosurgery was used. Anonymized patient images, structures and dose distributions derived using the two different registration methods were imported to an independent software for dose distribution, DVH analysis and comparison. Results Geometric differences of the order of 1mm (mean value: 0.9 ± 0.4 mm) between the two different registration methods were observed. These differences can considerably influence plan evaluation indices of both target and OARs leading to dose differences of the order of 10% in D95% values of target volume (mean value: 8 ± 6%). Dose differences of similar degree were observed in Dmax and D 30 mm 3 values of OARs. Conclusion Despite being relatively small (of the order of 1 mm), geometric differences between the two registration methods used in GK radiosurgery may affect considerably plan quality due to high dose gradients encountered in such applications.