1. A system ( 1 ) for registration of medical images ( 10 , 11 ), the system ( 1 ) comprising: a detecting module ( 13 ) adapted to detect one or more image areas ( 14 , 14 ′, 25 , 26 ) in a first image ( 11 ), the image areas ( 14 , 14 ′, 25 , 26 ) being insufficiently similar to corresponding image areas of a second image ( 10 ), a masking module ( 18 ) adapted to create at least one exclusion mask ( 22 , 24 , 27 ) to specify image pixels or voxels belonging to these insufficiently similar image areas ( 14 , 14 ′, 25 , 26 ), and a registration module ( 28 ) adapted to perform a registration between image areas of the first image ( 11 ) which are not included in the exclusion mask ( 22 , 24 , 27 ) and corresponding image areas of the second image ( 10 ).