Objective To assess the association between hypodontia and skeletal malocclusions in orthodontic patients. Materials and Methods This cross-sectional study comprised of orthodontic records of 40 hypodontic patients (12 males and 28 females) and 120 non hypodontic patients (58 males and 62 females) as control group matched for gender and age with the study sample who came to the orthodontic department for their treatment were selected. Orthopantamograms were evaluated for hypodontia, whereas lateral cephalogram were traced to determine the cephalometric parameters. The association between different classes of skeletal malocclusion and hypodontia was determined using Pearson’s Chi-square test and the cephalometric parameters between patients with hypodontia and without hypodontia (controls) were assessed using Student’s t-test. Result In hypodontic group, 19 (47.5%) patients had skeletal class II, 18 (45%) patients had skeletal class I, and only 3 (7.5%) patients had skeletal class III malocclusions. Whereas in non-hypodontic group (control group), 86 (53.75%) patients had skeletal class II, 63 (39.38%) patients had skeletal class I, and 11 (6.87%) patients had skeletal class III malocclusions. There was no statistical difference between hypodontia and different skeletal classes of malocclusions ( p = .654). Cephalometric parameters between the control group and hypodontic group did not reveal any significant difference ( p > .05). Conclusion This study did not find any association between different classes of skeletal malocclusions and hypodontia. The cephalometric skeletal parameters were not significantly different in hypodontic and control group. It is suggested that the patients having hypodontia will be evaluated on an individual basis for their treatment.