Objective: To examine the prevalence of congenital absence of permanent teeth other than third molar teeth in non-syndromic children in the Black Sea and Mediterranean Regions of Turkey, and the correlation between gender and distribution sites in the jaws. Material and Methods: Panoramic radiographs and clinical records of 9831 children (5025 girls, 4806 boys) in the Mediterranean Region and 11372 children (5540 girls, 5832 boys) in the Black Sea region were examined. All panoramic radiographs were evaluated by a dentist. The permanent tooth, which was not seen in radiography, was recorded as a congenitally missing tooth, and the fact that the tooth was not extracted was confirmed by treatment records. The data were statistically evaluated by Chi-Square and t-test. Results: The prevalence of congenitally missing permanent teeth was 2.8% (3.52% in girls, 2.5% in boys) in the Mediterranean region and 1.63% (1.82% in girls and 1.45% in boys) in the Black Sea region. Congenitally missing permanent teeth were observed more in the maxilla compared to mandible. The teeth that most frequently have congenitally missing permanent teeth in the Mediterranean Region are mandibular second premolars, maxillary lateral incisors and maxillary second premolars, respectively. The teeth that most frequently have congenitally missing permanent teeth in the Black Sea region are mandibular second premolars, maxillary second premolars and maxillary lateral incisors, respectively. Most of the patients had one or two teeth missing, and the lack of three or more teeth was rare. Conclusion: In this study, which is performed in different climatic characteristics of Black Sea and Mediterranean Regions, the frequency of congenitally missing teeth is similar.