Twelve new oltho-, meta- and para- chloro-(and bromo)-substituted derivatives of 2- and 4-benzylthio-6-methyluracils have been prepared in the reactions of 2- and 4-thio-6-methyluracil with the corresponding benzyl halides. Fl induced mass spectral fragmentation of these compounds was investigated. Fragmentation pathways are proposed on the basis of accurate mass and metastable transitions measurements. The correlation between the abundance of the M+. and the selected fragment ions of the investigated compounds is discussed. The data obtained create the basis for distinguishing structural isomers.