Objective　To explore the relationship of mutations in activin receptor-like kinase 1 gene (ALK1) and bone morphogenetic protein receptorⅡgene (BMPR2) with childhood idiopathic pulmonary arterial hypertension (IPAH). Methods　The DNA sample from 14 pediatric patients diagnosed clinically of IPAH and some of their family members were collected. The promoters and exons of ALK1 and BMPR2 gene were directly sequenced by the next generation sequencing. The results were compared with the sequence of ALK1and BMPR2 gene in GenBank. The mutant genes were verified by first generation sequencing. One hundred and six healthy children were recruited as controls. Results　A missense mutation in exon 3 of ALK1 gene (c.77C>T:p.P26L) was detected in one female IPAH patient, which is a new mutation site after searching database of HMGD. A missense mutation in exon 11 of BMPR2 (c.1447T>C:p.C483R) was detected in a female patient, a missense mutation in exon 5 of BMPR2 (c.621+8T>C) was detected in a male patient’s mother, and a missense mutation in exon 10 of BMPR2 (c.1322G>A:p.G441E) was detected in a female patient’s mother. These 3 missense mutations had been reported. Conclusions　A missense mutation in exon 3 of ALK1 gene is first discovered in IPAH patient of Han nationality, which may be responsible for the development of IPAH.