It is hypothesized that oligosaccharides are another potential source of immunological cross-reaction between different plant allergens. Patatin is the most abundant glycoprotein in potato and has been described to have an oligosaccharide of composition Man3(Xyl)GlcNAc2(Fuc). In this work, N-glycosylation profiles of patatin proteins isolated from tubers of different potato species were investigated and compared. Oligosaccharides were released by enzymatic digestion with PNAGase A and analyzed primarily by matrix-assisted laser desorption ionization mass spectrometry. For glycan labeling, a modified version of on-target derivatization with phenylhydrazine was applied. This study found the presence of glycan structures not described previously in patatins of potato tubers, and their glycan profiles significantly differed. This knowledge about the glycosylation of potato patatins may be helpful for correct choice of potato species to decrease the presence of specific glycan epitopes causing food allergy as well as for utilization of potatoes for the manufacture of therapeutic proteins.