A method and system for detection of native and bypass coronary ostia in a 3D volume, such as a CT volume, is disclosed. Native coronary ostia are detected by detecting a bounding box defining locations of a left native coronary ostium and a right native coronary ostium in the 3D volume using marginal space learning (MSL), and locally refining the locations of the left native coronary ostium and the right native coronary ostium using a trained native coronary ostium detector. Bypass coronary ostia are detected by segmenting an ascending aorta surface mesh in the 3D volume, generating a search region of a plurality of mesh points on the ascending aorta surface mesh based on a distribution of annotated bypass coronary ostia in a plurality of training volumes, and detecting the bypass coronary ostia by searching the plurality of mesh points in the search region.