Background Congenital absent digits continue to be described by many confusing terms and are currently classified in categories I, V, and VI of the International Federation of Societies for Surgery of the Hand classification and seven subclassification systems. Very few classification systems provide any logical basis for surgical reconstruction. The purpose of this study was to develop a simple alphanumerical documentation system to reproducibly describe the morphological or radiographic appearance of congenital absent digits and facilitate communication of these childrens' hand anomalies from one hand surgeon to another. Methods Dorsal and palmar photographs and PA radiographs of 235 hands in 204 children born with congenital absent digits over a 15-year period were analyzed to determine which digital rays were missing and their level of absence. Each hand can be described by three letters, R (radial), C (central), and U (ulnar), as well as numbers 1-5. The first letter and number designate which rays are missing and the second and third letters and numbers designate which rays remain present. Results There are 15 morphological phenotypes of congenital absent digits. The three most common phenotypes are U4R1 (a thumb but absence of all four fingers), R1U4 (absent thumb), and R5 (aplastic hand). Conclusions This new documentation system allows hand surgeons to describe the simple morphological or radiographic appearance of congenital absent digits; incorporates all the previous subclassification systems that have attempted to describe congenital absent digits in radial, central, and ulnar deficiencies, symbrachydactyly, and congenital constriction ring syndrome; and has subsequently allowed the development of an algorithm which predicts whether conventional or microsurgical reconstruction is indicated for each specific phenotype.