CDG Ia (phosphomannomutase deficiency) has a wide clinical spectrum with the most severe affected patients having multisystemic disease in addition to severe nervous system involvement. We report a patient with CDG Ia and an intermediate phenotype due to mild neurological impairment and borderline cognitive abilities despite the occurrence of typical extraneurological symptoms. These included liver involvement, coagulopathy and failure to thrive with enteropathy. Genotype analyses showed that he was compound heterozygous for T237R/C241S mutations. This observation underlines that the CDG Ia clinical spectrum may include intraindividual variability that might reflect different degrees of glycosylation abnormalities among distinct body compartments. CDG Ia should be considered in cases of unexplained liver involvement and/or enteropathy in patients with mild developmental delay and subtle neurological signs.