Di- and trisaccharides obtained by transgalactosylation reaction of lactose using two different commercial enzyme preparations (Pectinex Ultra SP-L and Lactozym 3000 L HP G) have been characterised by gas chromatography-mass spectrometry as their trimethylsilyl oximes. Although mass fragments are common for most of the glycosidic linkages, their relative abundances can be used to determine carbohydrate identity. Moreover, formation of galactosyl- and digalactosyl-glycerols from the reaction mixture of Pectinex Ultra SP-L with lactose has been described by first time. Evolution of these compounds during transgalactosylation reactions and their influence on galactooligosaccharides (GOS) synthesis have been also evaluated. © 2008 Elsevier Ltd. All rights reserved.