1,2,3-Triazoles and 1,2,3-thiadiazoles have been receiving permanent interest due to their exciting chemical reactivity and interesting biological properties including antibacterial, anticancer and antiviral activities. There are four compounds bearing 1H-1,2,3-triazole core in clinical studies which may appear in the market of drugs in nearest future. Definitely reliable methods of their identification and quantification should be developed by that time. Mass spectrometry showed itself as the most reliable method of analysis when dealing with trace levels of organic compounds in the mixtures and in the most complex matrices, including biological ones. In the present study tandem mass spectrometry was used to study fragmentation pathways of protonated and deprotonated molecules of isomeric 4,5-functionalized 1,2,3-thiadiazoles and 1,2,3-triazoles in conditions of electrospray ionization (ESI). A group of marker ions allowing differentiation between the targeted isomeric compounds was established. Besides, interconversion of these isomers into one another was studied in the gas phase in conditions mimicking these processes in solution.