Objective　To screen the mutations in coding region of DNAI1 and DNAH5 genes in heterotaxy syndrome in Chinese Han children. Methods　Children diagnosed with heterotaxy syndrome and healthy children were recruited clinically. Peripheral blood DNA was extracted for whole exon sequencing, and nucleotide variations in the coding region of DNAI1 and DNAH5 genes were detected. Sanger sequencing was performed to verify the mutation sites found by exon sequencing. The effect of site variation on protein function was analyzed by bioinformatics software Mutationtaster, SIFT and PolyPhen-2. Results　Exon sequencing results of 81 children with heterotaxy syndrome and 89 healthy children can be used for follow-up analysis. Three coding region mutation sites in each of DNAI1 and DNAH5 gene were found in 81 children with heterotaxy syndrome. Four (4.94%) children carried DNAI1 gene mutation, and 2 (2.50%) carried DNAH5 gene mutation. The mutation site was not found in 89 healthy children. Bioinformatics analysis suggests that the above mutation sites may destroy protein function. Conclusions The mutation rates of DNAI1 and DNAH5 gene in Chinese Han children with heterotaxy syndrome were 4.94% and 2.50%, respectively. DNAI1 and DNAH5 gene mutations may be associated with heterotaxy syndrome in Chinese Han children.