A medical system, a medical imaging apparatus, and a method of setting a 3-dimensional (3D) marker on a 3D image are provided. The medical imaging apparatus a display unit displaying a 3-dimensional (3D) ultrasound image generated by using 3D data a user input unit receiving first input information for selecting a predetermined point of the 3D ultrasound image and a processor detecting 3D geometry information of a 3D marker that corresponds to the predetermined point in the 3D data based on the first input information, and setting the 3D marker on the 3D image based on the 3D geometry information that is detected.
