Cleft lip and palate cases have been one of the most difficult cases to diagnose and treat in the orthodontic practice. Different diagnostic tools like lateral cephalograms, occlusal view x-rays, anterio-posterior view x-rays etc. have been used to diagnose the extent of the cleft. But these all are the 2-dimentional representations of the 3-dimentional structure. Also there are superimpositions of the structures of the other side. So, to overcome the disadvantages and to better diagnose the cases of cleft lip and palate a comparative study was done between 3-D Cone Beam CT and other diagnostic tools using a sample size of 10 cases of cleft lip and palate.