To date, sterylglucosides have been reported to be present in various fungi, plants, and animals. In bacteria, such as Helicobacter pylori, proton NMR spectral analysis of isolated 1-O-cholesteryl-β-d-glucopyranoside (GlcChol) demonstrated the presence of an α-glucosidic linkage. By contrast, in animals, no detailed structural analysis of GlcChol has been reported, in part because animal-derived samples contain a high abundance of glucosylceramides (GlcCers)/galactosylceramides, which exhibit highly similar chromatographic behavior to GlcChol. A key step in vertebrate GlcChol biosynthesis is the transglucosylation reaction catalyzed by glucocerebrosidase (GBA)1 or GBA2, utilizing GlcCer as a glucose donor. These steps are expected to produce a β-glucosidic linkage. Impaired GBA1 and GBA2 function is associated with neurological disorders, such as cerebellar ataxia, spastic paraplegia, and Parkinson's disease. Utilizing a novel three-step chromatographic procedure, we prepared highly enriched GlcChol from embryonic chicken brain, allowing complete structural confirmation of the β-glucosidic linkage by H-NMR analysis. Unexpectedly, during purification, two additional sterylglucoside fractions were isolated. NMR and GC/MS analyses confirmed that the plant-type sitosterylglucoside in vertebrate brain is present throughout embryonic development. The aglycon structure of the remaining sterylglucoside (GSX-2) remains elusive due to its low abundance. Together, our results uncovered unexpected aglycon heterogeneity of sterylglucosides in vertebrate brain.