Sugars are important molecules with remarkable cell signals pathway functions in higher organisms.The structural complexity of sugar represented by its isomeric, anomeric and diasteromeric configurationsdeserve the implementation of modern, rapid and sensitive methodologies for its identification and differentiation.Mass spectrometry and its analyzer of ion trap provide new alternative techniques that encouragethe control of the fragmentation energies supplied to molecules. Since stereoisomer differentiation isconsider outside the mass spectrometry domain, a methodology has been applied in order to differentiateβ-D-galactose, β-D-glucose and the disaccharides β-D-galactopyranosyl-(1→4)-β-D-glucopyranoside(lactose), α-D-glucopyranosyl-(1→4)-β-D-glucopyranoside (maltose) y β-D-fructofuranosyl-(2↔1)-α-D-glucopyranoside (sacarose) trough its ammonium and lithium adducts by infusion on ESI-IT-MS/MSmass spectrometer. Different fragmentation energies have been used to ensure the ion marker occurrencein the analyte stereochemistry. It is evident that the collision energies control in structural analysis ofmolecules provides a powerful and modern analytical tool to be applied in control laboratories.