This paper describes the application of the methylthiomethyl (MTM) protecting group for the N-1 position in differentially protected pyrrolo[2,3-d]pyrimidin-2,4-diones. By reaction of selected systems with SO2Cl2 at low temperature resulted in selective formation of N-1-chloromethyl derivatives. Subsequent heating in aqueous THF with silica gel afforded the deprotected compounds in good yield. Selectivity in the presence of N-3 methoxymethyl (MOM) and benzyloxymethyl (BOM), and N-7 p-nitrophenethyl protection was achieved.