OBJECTIVE To obtain new insights into aetiological backgrounds, and to search for diagnostic biomarkers by assessing the difference in urinary proteins between cats with spontaneous feline idiopathic cystitis (FIC) and healthy controls. MATERIALS Urine supernatants of 18 cats with FIC and 18 healthy control cats, and bladder biopsies of two FIC diseased cats and four healthy controls were included in the study. METHODS The Bradford method was used to determine protein quantity in urine supernatants. Urine was separated by two-dimensional (2-D) gel electrophoresis. Selected protein spots were excised from two-dimensional gels and analysed with tandem mass spectrometry. Validation of Trefoil factor 2 expression was realized with Western blot and immunohistochemistry. Western blot signal intensities were quantified with image quant software. RESULTS Eleven differentially expressed protein spots were identified between the 2-D gels of cats with FIC and control cats. Ten spots (only visible in the FIC gel) were identified as albumin and one spot (only visible in the control gel) was identified as Trefoil factor 2.Using quantification of Western blot signal intensities and immunohistochemistry a decrease in Trefoil factor 2 (TFF2) in cats with FIC could be revealed for the first time. CONCLUSION Deficiency in TFF2 possibly leads to impaired repairing abilities and immune response of the urothelium. The result could be a greater susceptibility to injury, inflammation and relapse. Therefore TFF2 deficiency might be an important event in FIC pathogenesis. Detection of a decrease in urinary TFF2 could serve as diagnostic biomarker, facilitating diagnosis. As FIC can serve as an animal model for human painful bladder syndrome/interstitial cystitis, the findings of this study might also be valuable for interstitial cystitis research and should be further investigated.