There is a growing interest on glycol-split low-molecular weight heparins (gs-LMWHs), obtained by periodate oxidation of LMWHs, optionally followed by borohydride reduction, as potential anticancer and anti-inflammatory drugs. However, their structural characterization is still a challenging task, mainly because of the high microheterogeneity of the starting material. In addition, susceptibility to oxidation of some end-groups of LMWHs induces additional heterogeneity, making analysis of gs-LMWHs more complex. In our previous study we showed that 1,6-anhydro-D-mannosamine N-sulfate was affected by periodate, while its epimer 1,6-anhydro-D-glucosamine N-sulfate was resistant. In order to understand the apparently anomalous behavior of terminal 1,6-anhydro-D-mannosamine N-sulfate residues, in the present work we have studied by NMR spectroscopy and LC/MS the behavior of the reducing end amino sugar residues of the tetrasaccharides, isolated from the LMWH enoxaparin, in the presence of periodate. Their molecular mechanics conformational characterisation has been also performed. We have shown that the C(2)–C(3) bond of the 1,6-anhydro-D-mannosamine residue can be split by periodate despite the N-substitution. Moreover, we have found that both terminal D-mannosamine N-sulfate and D-glucosamine N-sulfate, lacking the 1,6-anhydro-bridge, can be also oxidized by periodate but with significantly lower rate. The present results suggest that the cis-e-/a-position of OH and NHSO3− groups of N-sulfated 1,6-anhydro-D-mannosamine is not the only factor that makes these end residues susceptible to the oxidation. The 1,6-anhydro-bridge that “blocks” the ring conformation appears another crucial factor for oxidation to occur. Moreover, we have shown that controlling the reaction time could permit to selectively split non-sulfated iduronic acids of enoxaparin chains without oxidizing terminal amino sugar residues, a finding that may be useful to obtain more structurally homogeneous gs-LMHWs.