Congenitally missing permanent teeth was evaluated on orthopantomograms of 611 apparently healthy patients, aged 10 to 25 years at a specialist dental clinic in Lagos, Nigeria. The prevalence of congenitally missing teeth (CMT) including third molars was 7.3% in boys and 10.7% in girls, and 9.3% for both sexes combined. There were in total 57 CMT, and on average 2.1 permanent teeth were missing per child. The most commonly absent tooth was the maxillary lateral incisor (n = 22), followed by equal number of maxillary and mandibular third molars (n = 21), then mandibular second premolars (n = 19). On the other hand, no first and second molars were missing, and there were no cases with oligodontia (6 or more CMT excluding the third molar). Symmetry of CMT was predominant with 43 pairs (72.3%) of bilateral symmetry recorded. The distribution of CMT either between the maxilla and the mandible, or between the right and left quadrant did not show any significant association with sex (P > 0.05).