(1) Background: Tooth agenesis is one of the most common developmental dental anomalies often affecting the maxillary incisors area and premolar regions. (2) Purpose: The aim of this study was to assess the prevalence and distribution of permanent tooth agenesis and the associated dental abnormalities among orthodontically treated children. (3) Materials and Methods: This study was carried out utilizing 3000 pretreatment records of children who underwent orthodontic treatment, 1780 (59%) females and 1220 (41%) males, aged 10-25 years (mean age 15 years). Tooth agenesis and other dental anomalies were surveyed using their panoramic radiographs, according to gender, pattern, and location. The level of statistical significance was set at < 0.05 using -test or Chi-Square tests. (4) Results: The total number of missing teeth, excluding third molars, was 518 (17%) found in 326 (11%) children. The majority were the maxillary lateral incisors, which was 176 teeth (34%) ( < 0.05). Of them, 111 (63%) were in females, and 65 (37%) were in males. The second most common missing tooth was mandibular second premolars, which was 137 teeth (26%), followed by missing 73 (14%) maxillary second premolars. Impacted teeth had the highest associated dental anomaly prevalence (14.3%), while transposition showed the lowest anomaly prevalence (0.5%). (5) Conclusions: A prevalence of 11% for tooth agenesis was detected in this study. More teeth were missing in the maxilla compare with the mandible. A significant association was found between missing maxillary lateral incisors and missing premolars ( < 0.05). Associated dental anomalies included an increased number of peg-shaped maxillary lateral incisors, palatally displaced and impacted maxillary canines, ectopic teeth, and infra-occluded (submerged) primary second molars.