A Japanese boy had clinical features of congenital disorder of glycosylation type Ia (CDG Ia, also known as carbohydrate-deficient-glycoprotein syndrome, previously), and enzymatic and molecular assay of phosphomannomutase confirmed this diagnosis. During infancy, the patient showed delayed mental and motor development, hypotonia, ataxia, hepatomegaly, liver dysfunction, abnormal coagulation system and cerebellar hypoplasia. At present, though he is 3 years and 8 months old, he cannot utter meaningful words or sit by himself. These findings suggested that he had one of the severe phenotypes of Japanese CDG Ia. Mutational analysis demonstrated heterozygosity for the missense mutation in exon 4 (P113L) and a novel nonsense mutation in exon 7 (R194X). We report his clinical course and the results of molecular assay, and discuss correlation between clinical severity and genotype.