A method and apparatus for performing registration of medical images includes mapping a virtual coordinate system used by a first medical apparatus and a virtual coordinate system used by a second medical apparatus to one another. The coordinate systems are associated with a real-time medical image captured by the first medical apparatus and a three-dimensional (3D) medical image previously captured by the second medical apparatus, respectively. The method further includes detecting a position of a probe of the first medical apparatus from a coordinate system used by the second medical apparatus, based on a result of the mapping, determining a volume image corresponding to the detected position of the probe from the previously captured 3D medical image, and extracting from the determined volume image a cross-sectional image corresponding to the real-time medical image, where the real-time medical image changes according to a patient's physical movement.