Abstract The mass spectral fragmentation of twelve new 2-alkoxycarbonylalkylthio substituted derivatives of uracils is discussed and fragmentation pathways, elucidation of which were assisted by accurate mass measurements and metastable transitions are proposed. It has been found that the basic mass spectral fragmentation of these compounds is due to cleavage of S [BOND] C math image, O [BOND] C math image and C math image ...