Objective　To explore clinical manifestations, genetic diagnosis and treatment of childhood alternating hemiplegia. Methods　Two patients were clinically diagnosed as alternating hemiplegia. ATP1A3 gene sequencing was performed on these two children and their parents. Literatures on childhood alternating hemiplegia were reviewed. Results　Both patients were female. The first symptom of the first girl was alternating hemiplegia occurring at 4-month-old. For the second girl, the first symptom was seizure occurred at 6-month-old, and the typical symptoms including alternating hemiplegia occurred at the second year of course. Heterozygous missense mutations of c.2401G>A (p.D801N) and c.2731G>C (p.A911P) were found in ATP1A3 gene of these two girls, the latter hasn’t been reported in the Human Gene Mutation Database (HGMD) Professional. Conclusions　ATP1A3 gene sequencing should be conducted for children clinically diagnosed as alternating hemiplegia, which has important significance for diagnosis and genetic counseling.