The large scale synthesis of three orthogonally protected monosaccharide scaffolds suitable for use in the solid phase preparation of large diversity libraries is presented. Scaffolds based on 2-amino-2-deoxy-d-glucopyranose, 2-amino-2-deoxy-d-allopyranose, and 2,4-diamino-2,4-dideoxy-d-galactopyranose were prepared in good yield and with minimal chromatographic purification from commercially available methyl 2-azido-2-deoxy-1-thio-β-d-glucopyranose and methyl 2-amino-2-deoxy-1-thio-β-d-glucopyranose.