As carbohydrate-deficient glycoprotein syndromes (CDGS) are multisystemic disorders with impaired central nervous function in nearly all cases, we tested isoforms of β-trace protein (βTP), a ‘brain-type’ glycosylated protein in cerebrospinal fluid (CSF) of nine patients with the characteristic CDGS type I pattern of serum transferrin. Whereas the serum transferrin pattern did not discriminate between the various subtypes of CDGS type I (CDGS type Ia, type Ic and patients with unknown defect), βTP isoforms of CDGS type Ia patients differed from that of the other CDGS type I patients. The percentage of abnormal βTP isoforms correlated with the severity of the neurological symptoms. Furthermore, two patients are described, who illustrate that abnormal protein N-glycosylation can occur restricted to either the ‘peripheral’ serum or the central nervous system compartment. This is the first report presenting evidence for an N-glycosylation defect restricted to the brain. Testing βTP isoforms is a useful tool to detect protein N-glycosylation disorders in the central nervous system.