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Alagille syndrome (ALGS) is a rare autosomal dominant (AD) genetic disorder. It is a multisystemic disease which involves liver, heart, skeleton, eyes, kidneys and skeletal abnormalities. The disease may involve a particular system like facial dysmorphism, cardiac or musculoskeletal system. Some individual may not have hepatic involvement. Here we report unusual case of 9-year-old boy with large ostium secundum atrial septal defect (16 mm) and branch pulmonary artery stenosis (Left). The boy had facial dysmorphism (broad forehead, frontal bossing, triangular facies, hypertelorism, prominent ear and pointed chin, straight nose with bulbous tip). His psychological assessment revealed borderline IQ. He also had butterfly vertebrae in thoracic and lumber region which was found incidentally. He underwent device closure for atrial septal defect and balloon pulmonary valvuloplasty for left pulmonary artery stenosis. Both the procedure was performed simultaneously without complications. As there is no curative management for the disorder so symptomatic management is the only treatment option. We suggest screening of suspected individual, so that early intervention can safe patient from devastating complications of involved organ system.