1. A computer-implemented method for automatically registering during an operative procedure a three dimensional (3D) pre-operative image of a heart with intra-operative electrophysiological (EP) points of a 3D electro-anatomical (EA) image map of the heart, the method performed by the computer comprising the steps of: providing a segmented triangulated surface of the heart extracted from the pre-operative 3D image of the heart; acquiring one or more EP points of the heart during an operative procedure; selecting at least one EP point associated with a first cardiac chamber, and a first corresponding point on a surface of said first cardiac chamber from said segmented triangulated surface; using said first corresponding points to register during said operative procedure the segmented triangulated surface of said first cardiac chamber with the EP points associated with said first cardiac chamber; selecting at least one or more EP points associated with a second cardiac chamber, and second corresponding points on a surface of said second cardiac chamber from said segmented triangulated surface; and using said second corresponding points to register during said operative procedure the segmented triangulated surface of said second cardiac chamber with the EP points associated with said second cardiac chamber, wherein the registration of said segmented triangulated surface of said first cardiac chamber with the EP points associated with said first cardiac chamber are used to initialize the registration of the segmented triangulated surface of said second cardiac chamber with the EP points associated with said second cardiac chamber, and wherein the registration of said segmented triangulated surface of said first and second cardiac chambers with EP points associated with said first and second cardiac chambers is represented by a rigid transformation matrix.