The reaction of aliphatic esters with methylthiocyanate and triflic anhydride affords substituted 4-alkoxy-2,6-bis(methylthio)pyrimidines with minor amounts of substituted S-methyl N-alkanoylthiocarbamates. The structure of the starting ester appears to determine the ratio of final products. Methylthio groups on the pyrimidine ring can be easily converted into methylsulfonyl groups by oxidation. Controlled