Sulphonamides are antibacterial compounds used extensively in farming and veterinary practice. Residues are commonly found in meat and milk. The growing concern about antibiotic resistance of bacteria led to a lowering of the legal concentration limits of sulphonamides in food. A range of analytical methods, employing tandem mass spectrometry (MS/MS) and selected reaction monitoring (SRM), have been developed to allow screening at the limit of detection (LOD) levels. Interest was drawn to the fragment ions produced by the sulphonamides, some involving complex rearrangements that have not previously been looked at. Here we report an investigation into the fragmentation pattern of sulphonamides under electrospray (ES) MS/MS conditions using ion trap and Fourier transform ion cyclotron resonance (FTICR) mass spectrometers. Structures are proposed for the main fragment ions observed for a range of sulphonamides, the effects of the functional groups in the dissociation pathway of the compounds are investigated, and the mechanisms leading to the main fragment ions are explored.