The number of putative glycosyltransferase genes in Drosophila melanogaster is estimated to be around 100—approximately half the number identified in the human genome. Enzymatic activity has been experimentally confirmed for about half of these genes, while the remainder remain functionally uncharacterized. Roughly half of the Drosophila glycosyltransferase genes have identifiable human orthologs, which are either known or predicted to synthesize glycan structures conserved between Drosophila and humans. Comprehensive genetic resources—including loss-of-function mutants, RNA interference lines, and CRISPR/Cas9-mediated knockout lines—are readily available from Drosophila stock centers in Japan and internationally. These tools facilitate systematic in vivo functional analyses of individual glycosyltransferases. Studies in Drosophila have revealed essential roles for glycosylation in development, neural function, immunity, and cell signaling. Many of these glycan-related functions have been subsequently validated in mammalian systems, highlighting the utility of Drosophila as a genetically tractable and evolutionarily conserved model organism for glycoscience. Moreover, Drosophila is increasingly being employed to investigate the molecular pathogenesis of rare and undiagnosed human diseases. By expressing human disease-associated gene variants in fly tissues—such as the compound eyes or wings—researchers can assess their functional impact through phenotypic outcomes. Notably, several Drosophila models of congenital disorders of glycosylation have already been established and characterized. This approach not only advances mechanistic understanding but also supports the functional interpretation of variants of uncertain significance in clinical genetics.