Pulmonary hypertension is a potentially lethal condition, which affects adults and children alike. Genetic factors are implicated in the causation of primary pulmonary hypertension. We investigate the role of polymorphism in the 5HTT gene in the etiology of pulmonary hypertension in children aged 1-18.8 years. We have tested the hypothesis that the 5HTT gene does contribute to the pathogenesis of this disease in children by comparing the allelic frequencies of both the long and short variants between children with idiopathic pulmonary hypertension and pulmonary hypertension secondary to underlying pulmonary disease. We found that homozygosity for the long variant of 5HTT was highly associated with idiopathic pulmonary hypertension in children, suggesting perhaps a more important role for 5HTT gene function in the pathogenesis of early onset disease. (c) 2005 Elsevier Inc. All rights reserved.