Objective　To report a case of microcephaly with a novel mutation in ASPM gene, and to explore the value of gene examination in the diagnosis and treatment of the disease. Methods　Clinical data of a one year and 6 months old girl with microcephaly was retrospectively analyzed, and whole exome of microcephaly-related genes were detected by second generation sequencing. The literature of microcephaly was reviewed. Results　There were two novel mutations in exons 18 (c.8815delA) and exon 3 (c.C1789T) in ASPM gene. Bioinformatics software (Mutation Taster) predicted these two variants were pathogenic. Conclusion　The c.8815delA mutation in exon18 of ASPM gene and the c.C1789T mutation in exon 3 may be one of the causes of primary microcephaly in children. Early gene examination is helpful for early diagnosis of the disease.