The structure of the defective transferrin in carbohydrate-deficient glycoprotein syndrome was characterized. Structurally abnormal sugar chains were not found in reversed phase chromatograms of pyridylaminated derivatives from the transferrin of two patients in different families. Electrospray ionization mass spectrometry of the whole transferrin molecules revealed an abnormal species that was smaller than normal tetrasialotransferrin by 2,200 daltons, just the size of the disialylated biantennary sugar chain. These data indicated that the disialotransferrin specifically found in this syndrome is missing either of two N-linked sugar chains, suggesting a metabolic error in the early steps of protein glycosylation.