To estimate the prevalence of congenitally missing teeth (CMT) in patients evaluated for orthodontic care. A sample of 668 panoramic radiographs from Mexican population was reviewed from orthodontic healthy patients, 9-20 years old. Statistical tests were used to compare maxillary and mandibular hypodontia in right and left quadrants between males and females. Prevalence was 27% when all teeth were included, and was 2.7% when third molars were excluded. A significant difference was found between maxillary and mandibular symmetrical CMT in third maxillary molars, lateral incisors and second premolars (P < 0.001), and in mandibular third molars and central incisors (P < 0.001). We confirmed that occurrence of CMT in the permanent dentition of a Mexican population most often affects third molars, followed by maxillary lateral incisors and then mandibular second premolars.