The purpose of this study was to investigate the prevalence and patterns of congenitally missing teeth in permanent teeth excluding third molars, in patients aged 8 to 16 years who visited Pusan National University Dental Hospital from January 2010 to February 2021. This retrospective study evaluated tooth agenesis and the pattern of missing teeth represented by the tooth agenesis code by reviewing panoramic radiographs and electronic medical records of 11,759 patients, including 5,548 females and 6,211 males. The prevalence of congenitally missing teeth was 10.74% (females 11.95%, males 9.66%, <i>p</i> < 0.0001). Patients with tooth agenesis had an average of 2.22 missing teeth, and congenitally missing teeth occurred more frequently in the mandible (8.39%) than in the maxilla (4.52%, <i>p</i> < 0.0001). The mandibular second premolar (58.19%) was the most frequently missing tooth. The second premolar was the most frequently missing tooth in all quadrants (30.10%, 31.67%, 43.14%, and 35.59%) when a single tooth was absent, while the first and second premolars were the most commonly absent teeth (11.69%, 11.47%, 5.94%, and 5.24%) when two or more teeth were missing. In the relationship between maxillarymandibular antagonistic quadrants and full mouth, the 1st to 4th place of the missing patterns were all involved with the 1st and 2nd premolars. This study can be clinically helpful in establishing a treatment plan for patients with missing teeth. In addition, it can be used as basic data for molecular biological research to find out the relationship between tooth agenesis and specific genes.