In landmark-based image registration, estimating the landmark correspondence plays an important role. In this letter, a novel landmark correspondence estimation technique using mean shift algorithm is proposed. Image corner points are detected as landmarks and mean shift iterations are adopted to find the most probable corresponding point positions in two images. Mutual information between intensity of two local regions is computed to eliminate mis-matching points. Multi-level estimation (MLE) technique is proposed to improve the stability of corresponding estimation. Experiments show that the precision in location of correspondence landmarks is exact. The proposed technique is shown to be feasible and rapid in the experiments of various mono-modal medical images.