Purpose Although the Oberg-Manske-Tonkin (OMT) classification has been recommended by the International Federation of Societies for Surgery of the Hand owing to some insufficiencies of the Swanson classification system, it has not achieved a universal adoption by hand surgeons. In this study, we hypothesize that the OMT classification can be used easily to classify congenital upper extremity anomalies. We also aim to make epidemiological analysis of congenital upper extremity anomalies with the OMT classification and to compare the applicability of the OMT and the Swanson classifications. Methods We retrospectively analyzed 711 patients and 833 extremities operated on between 2012 and 2017. Photographs, plain x-rays, and brief medical histories of the patients were evaluated by 4 plastic surgeons. Two independent evaluations were made by each surgeon in 1-month interval using these classification systems. Results Total number of upper extremity anomalies recorded was 1050. Of the 711 patients operated on, 122 had bilateral anomalies. The anomalies were identified in 833 extremities because many extremities had more than a single diagnosis. We were able to classify all of the anomalies within the OMT classification. The OMT classification gives better reliability results compared with the Swanson classification according to intrarater and interrater reliabilities. Conclusions Compared with the Swanson classification system based on phenotypic evaluation of the extremity, the OMT classification system is easier to apply and the association of the anomaly with the embryologic origin during evaluation is possible. We believe that multiple studies from different centers will boost the international acceptance of the OMT classification.