An automated carbohydrate-synthesizer (glycoconjugate-synthesizer) "Golgi^TM" was developed by mimicing biosynthetic system of the Golgi apparatus in cells. The system was improved by using tailored-magnetic beads for immobilizing glycosyltransferases and fine-filter membrane system to achieve fully-automated synthesis in 36 or 96-well reaction vessels. It was demonstrated that combined use of "Golgi^TM" with a conventional peptide-synthesizer gives high throughput parallel synthesis of biologically important glycopeptides.