Background Congenital disorders of glycosylation (CDG) are a growing group of rare genetic disorders. The most frequently used screening method is sialotransferrin profiling using isoelectric focusing (IEF). Capillary zone electrophoresis (CZE) may be a simple and fast alternative. We investigated the Capillarys™ CDT assay (Sebia, France) to screen for N-glycosylation disorders, using IEF as gold standard. Methods Intra- and inter-assay precision were established, and analyses in heparin-anticoagulated plasma and serum were compared. Accuracy was assessed by comparing IEF and CZE profiles of 153 samples, including 49 normal, 53 CDG type I, 2 CDG type II, 1 combined CDG type I and type II and 48 samples with a Tf-polymorphism. Neuraminidase-treated plasma was analysed to discriminate CDG and Tf-polymorphisms using samples of 52 subjects (25 had a confirmed Tf-polymorphism). Age-dependent reference values were established using profiles of 312 samples. Results Heparin-plasma is as suitable as serum for CDG screening with the Capillarys™ CDT assay. The precision of the method is high, with a limit of quantification (LOQ) of 0.5%. All profiles, including CDG and Tf-polymorphisms, were correctly identified with CZE. Forty-nine of 52 neuraminidase-treated samples correctly identified the presence/absence of a Tf-polymorphism. Interferences in 3/52 samples hampered interpretation. Sialo-Tf profiles were dependent of age, in particular in the first three months of age. Conclusions CZE analysis with the Capillarys™ CDT kit (Sebia) is a fast and reliable method for screening of N-glycosylation defects. Tf-polymorphisms could be excluded after overnight incubation with neuraminidase.