The free-living nematode Caenorhabditis elegans is a well-characterized eukaryotic model organism. Recent glycomic analyses of the glycosylation potential of this worm revealed an extremely high structural variability of its N-glycans. Moreover, the glycan patterns of each developmental stage appeared to be unique. In this study we have determined the N-glycan profiles of wild-type embryos in comparison to mutant embryos arresting embryogenesis early before differentiation and causing extensive transformations of cell identities, which allows to follow the diversification of N-glycans during development using mass spectrometry. As a striking feature, wild-type embryos obtained from liquid culture expressed a less heterogeneous oligosaccharide pattern than embryos recovered from agar plates. N-glycan profiles of mutant embryos displayed, in part, distinct differences in comparison to wild-type embryos suggesting alterations in oligosaccharide trimming and processing, which may be linked to specific cell fate alterations in the embryos.