Feline idiopathic cystitis (FIC) is a common lower urinary tract disorder in cats, which often recurs. Published reports document increased urine fibronectin and thioredoxin concentrations in cats with FIC compared with healthy control cats. Therefore, these proteins might be of interest in the pathophysiology of FIC. The purpose of the present study was to evaluate variations in these urine proteins throughout the course of FIC by assessing their concentrations in urine specimens from cats with a history of obstructive FIC. Urine total protein (TP) was measured using the Bradford assay, while urine fibronectin and thioredoxin concentrations were determined by Western blot analysis. Urine TP was significantly higher in cats with obstructive FIC at presentation (day 0) than in healthy control cats (P<0.01). There were significant decreases in urine TP in cats with obstructive FIC after 3months (P<0.01). Significantly higher urine fibronectin (P<0.01) and thioredoxin (P<0.05) concentrations were demonstrated in cats with FIC at day 0 compared to control cats, but there was no significant change over time (P>0.05). Increased concentrations of these proteins over time might reflect ongoing structural and pathological alterations to functional processes in the urinary bladders of cats with obstructive FIC.