Galactooligosaccharides are non-digestible carbohydrates with potential ability to modulate selectively the intestinal microbiota. In this work, a detailed characterization of oligosaccharides obtained by transgalactosylation reactions of the prebiotic lactulose, by using β-galactosidases of different fungal origin (Aspergillus oryzae, Aspergillus aculeatus and Kluveromyces lactis), is reported. Oligosaccharides of degree of polymerization (DP) up to 6 were detected and quantified by HPLC-ESI MS from a complex mixture produced by transgalactosylation reaction with A. oryzae (GOSLuAo), whereas only carbohydrates up to DP4 and DP5 were found for those obtained from the reaction with β-galactosidases from K. lactis (GOSLuKl) and A. aculeatus (GOSLuAa), respectively. Disaccharides (galactosyl-galactoses and galactosyl-fructoses) and trisaccharides were characterised in the three mixtures by GC-MS as their trimethylsilyl oximes. Galactosyl- and digalactosyl-glycerols were produced during the transgalactosylation reaction of lactulose with β-galactosidases from A. aculeatus and K. lactis, due to the presence of glycerol as enzyme stabiliser.