A variety of congenital syndromes affecting the face occur due to defects involving the first and second BAs. Radiographic evaluation of craniofacial deformities is necessary to define aberrant anatomy, plan surgical procedures, and evaluate the effects of craniofacial growth and surgical reconstructions. High-resolution CT has proved vital in determining the nature and extent of these syndromes. The radiologic evaluation of syndromes of the first and second BA should begin first by studying a series of isolated defects (cleft lip with or without CP, micrognathia, and EAC atresia) that compose the major features of these syndromes and allow a more specific diagnosis. After discussion of these defects and the associated embryology, we discuss PRS, HFM, ACS, TCS, Stickler syndrome, and VCFS.