Pompe disease is an autosomal recessive disorder caused by deficiency of the lysosomal enzyme acid alpha-glucosidase (GAA). Early and precise diagnosis can be highly important for the treatment, genetic counselling and prenatal diagnosis of this disease in potential candidates. Considering that Pompe disease studies have not been frequently conduced in China, to better understand the clinical course and molecular defects among this group, our study examined 21 Chinese patients with classic infantile Pompe disease. The median age of symptom onset in the patients was 2.5 months (0–7 months), and the median age of confirmed diagnosis was 5.6 months (2–12 months). GAA gene mutation analysis revealed 17 different mutations, two of which were novel (c.538C>A and c.2096T>C). The most frequent mutation in these patients was c.1935C>A, accounting for 40.5% (17/42 alleles) of the mutations. These results confirm the high prevalence of the c.1935C>A mutation in Chinese patients with classic infantile Pompe disease. Furthermore, identification of the novel alterations in the GAA gene will help to broaden the spectrum of the GAA mutations causing Pompe disease and to better understand the potential pathogenic role of each change.