BACKGROUND: Hypodontia or congenitally missing teeth is among dental anomalies with different prevalence in each region. The aim of this study was to evaluate the prevalence of congenitally missing permanent teeth in Iranian population. MATERIALS AND METHODS: A descriptive, retrospective and cross-sectional study was done. Panoramic radiographs of 2422 Iranian patients (1539 girls and 883 boys), 7-25 years old, were collected. The radiographs were studied for evidence of congenitally missing teeth. Data were analyzed using Paired t-test, Mann-Whitney test, Fisher exact test and Chi-square test (α = 0.05). RESULTS: Prevalence of congenitally missing teeth was totally 45.7% and 34.8% for third molars. The most frequent congenitally missing teeth was mandibular second premolars (23.34%) followed by maxillary second premolars (22.02%). Upper jaw showed significantly higher number of congenitally missing teeth (P value < 0.001). According to Chi-square test, congenital missing teeth was found approximately 10.9% in both females and males and there were no statistically significant difference between sexes (P = 0.19). CONCLUSION: The prevalence of congenitally missing teeth (CMT) in Iranian permanent dentition was 10.9%. The most common congenitally missing teeth were mandibular second premolar fallowed by maxillary second premolars.