Caudate nucleus (CN) is a specialized part of the dorsal striatum of each brain hemisphere involved in numerous cognitive processes. Caudate dysfunctions are associated with Alzheimer’s, Parkinson’s and Huntington’s disease, autism, and even schizophrenia. Most of the studies upon CN and related diseases were conducted using neuroimaging techniques, which, in some instances have reached contradictory conclusions. This state-of-the-art technique triggered the development of methods able to provide information at the molecular level. In this context, here we have implemented high resolution (HR) mass spectrometry (MS) and multistage MS (MSn), for mapping and structural analysis of gangliosides in human CN. Due to the high resolution and mass accuracy (average value: 1.5 ppm), 100 distinct species, of which 90 were di-, tri-, tetra-, and pentasialylated and 17 fucosylated and acetylated and, for the first time, species modified by CH3COO−, were reliably identified in the native CN ganglioside extract. Additionally, two structurally-relevant species, GD2 (d18:1/18:0) and GD2 (d18:1/16:2), were characterized with MS2–MS3 by collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD). The set of data collected by high-resolution mass spectrometry (HR-MS) revealed a much higher complexity of the CN ganglioside pattern than ever reported, and the species associated to this brain region, potentially implicated in many of its functions.