Branchio-oculo-facial syndrome represents a craniofacial disorder in which affected patients may develop a wide range of distinctive features that include cleft lip and/or palate, cervical aplastic skin defect, malformed pinna, and ocular anomalies. This study reports four new cases confirmed by the identification of mutations in the TFAP2A gene and describes in detail the findings in the craniofacial region. The four cases included two familial and two sporadic, and three have been followed since the birth. Two out of the four cases showed atypical features. One patient presented brainstem immaturity with dysregulation of sympathetic and parasympathetic systems, which have so far not been described in the literature and were associated with anxiety, panic attacks, and tiredness. Another patient had as an additional feature a hypoplastic thumb with distal implantation.