Fragmentation studies of three antifungal drugs, clotrimazole, fluconazole and clioquinol ,were performed. A triple quadrupole linear ion trap mass spectrometer was used for this purpose. This type of equipment enables MS3 spectra to be obtained which lead to better understanding of fragmentation pathways. Nevertheless, it is rarely used for fragmentation studies. The results obtained here for the antifungal drugs gave further insight into fragmentation pathways of clotrimazole and fluconazole. Moreover, fragmentation of clioquinol was investigated which had not been presented before. Copyright © 2011 John Wiley & Sons, Ltd.