The objective of this work was use of silybin nanoparticles in treatment of ulcerative colitis (UC). Eudragit RL PO nanoparticles loaded with silybin were produced using solvent-evaporation emulsification technique. Then, they were coated by Eudragit FS30D. Drug release was studied in different physiological environments. Colitis was induced by 4% of acetic acid in rats which received freeze-dried nanoparticles of silybin (75 mg/kg/day), dexamethasone (1 mg/kg/day), blank nanoparticles and normal saline orally for 5 days. Then macroscopic, histopathological evaluation and biochemical analysis, including myeloperoxidase (MPO) activity, tumor necrosis factor-a (TNF-alpha) and interleukin-6 (IL-6) levels in colon tissues were determined using enzyme-linked immunosorbent assay (ELISA) kits. Macroscopic and histopathological scores were improved by the optimised nanoparticles. The optimised nanoparticles had a particle size of 109 +/- 6 nm, zeta potential of 15.4 +/- 2 mV, loading efficiency of 98.3 +/- 12% and release efficiency of 40.8 +/- 5.5% at 24 h. TNF-alpha, IL-6 and MPO activity were reduced significantly by nanoparticles compared to control group (p<0.05).