Introduction: Three-dimensional evaluation and comparison of condyle-fossa relationship, their position and symmetry using CBCT in various sagittal skeletal malocclusions. Aims and Objectives: To evaluate and compare the size and morphology of right and left fossa and condyle, condyle-fossa relationship, position and symmetry in various malocclusions. Materials and Methods: Sixty eight subjects with a mean age of 18.2±3.5 years, were divided into three sagittal Skeletal malocclusion (Class I,Class II. Class III) groups. 15 Linear and 2 Angular variables were evaluated from the CBCT images obtained from Carestream CS 9300C 3D system. The digitization and measurements were carried out using Trophy Dicom CS 3D software. Statistical Analysis: Independent t test and Karl Pearsons coefficient of correlation. Results: On comparison between the Right and Left sides, Angle Md.Co.Pro-MS Plane in Group I (p=0.007**)and C.Co-MS Planein Group II (p=0.047*)was significant. On Comparison of Concentric positioning of condyles, the mean differences in Group II on the Right side (p =0.039 *) and on the Left side (p =0.004**) were significant. Conclusion: In Skeletal Class I malocclusion, width and height of condyle was increased on the left side. Anterior joint space was decreased significantly in Skeletal Class II malocclusion. Superior joint space was significantly decreased and width of mandibular fossa was increased on both the sides in Skeletal Class III malocclusion. The condyles were anteriorly placed in all skeletal malocclusions but greatest difference was present in Class II.