We previously reported that sequence and partial linkage information, including chain and blood-group types, of reducing oligosaccharides can be obtained from negative-ion electrospray CID MS/MS on a quadrupole-orthogonal time-of-flight instrument with high sensitivity and without derivatization (Chai, W.; Piskarev, V.; Lawson, A. M. Anal. Chem. 2001, 73, 651-657). In contrast to oligonucleotides and peptides, oligosaccharides can form branched structures that result in a greater degree of structural complexity. In the present work we apply negative-ion electrospray CID MS/MS to core-branching pattern analysis using nine 3,6-branched and variously fucosylated oligosaccharides based on hexasaccharide backbones LNH/LNnH as examples. The important features of the method are the combined use of CID MS/MS of singly and doubly charged molecular ions of underivatized oligosaccharides to deduce the branching pattern and to assign the structural details of each of the 3- and 6-branches. These spectra give complimentary structural information. In the spectra of [M - H]-, fragment ions from the 6-linked branch are dominant and those from the 3-linked branch are absent, while fragment ions from both branches occur in the spectra of [M - 2H]2-. This allows the distinction of fragment ions derived from either the 3- or 6-branches. In addition, a unique D2beta-3 ion, arising from double D-type cleavage at the 3-linked glycosidic bond of the branched Gal core residue, provides direct evidence of the branching pattern with sequence and partial linkage information being derived from C- and A-type fragmentations, respectively.