Objective. Patients with hypodontia are relatively common in clinical dentistry. This study was performed to determine the prevalence of hypodontia of permanent teeth in Korean orthodontic patients and whether such prevalence is associated with the type of dental clinic, patient gender, or the type of malocclusion. Materials and Methods. Over a five-year period, we evaluated 3,055 patients (mean age, 15.1 years; range 9~30) from two geographically separated orthodontic clinics: 1,479 from University Hospital and 1,576 from a private clinic. Hypodontia was diagnosed using panoramic radiographs, clinical examination, and dental casts. Results. The overall prevalence of hypodontia, excluding the third molars, was 11.3%, and there was no statistically significant association with the type of dental clinic, gender, or malocclusion patterns. The most commonly missing teeth were the mandibular second premolars (44.2%), followed by the mandibular lateral incisors (36.6%), and the maxillary second premolars (34.0%). In both sexes, 86.0% of patients with hypodontia were missing one or two teeth. Conclusion. The relatively high prevalence of hypodontia emphasizes the importance of dental examination in early childhood with radiographic screening for hypodontia as standard public oral health policy and warrants further investigation of the orthodontic treatment strategies to prevent resultant oral health impairments of hypodontia.