We report a rare case of a neonatal girl who presented with coughing and dyspnea immediately after feeds. At birth, she was noted to have an imperforate anus with a posterior fourchette fistula from which she was stooling. Initial imaging with radiography showed a normal bowel gas pattern; however, lumbar vertebral anomalies were noted. An upper GI series was performed and revealed a laryngeal cleft and malrotation. Ultrasound confirmed malrotation with an abnormal SMA-SMV relationship. Since laryngeal cleft is a rare condition and may not be known to most radiologists, its incidence is likely underestimated. It is important to note the association of laryngeal clefts with VACTERL and malrotation. In addition, it is essential not to confuse a laryngeal cleft with a tracheoesophageal fistula since the management differs.