The aim of our study was to assess the presence and degree of intestinal leakage in subjects suffering from short bowel syndrome (SBS) and its modification by parenteral nutrition. To this end we assessed circulating levels of selected makers of intestinal permeability including zonulin, fatty acid binding protein 2 (FABP-2), citrulline and glucagon-like peptide 2 (GLP-2). We also measured lipopolysaccharide binding protein (LBP) as a marker of circulating levels of lipopolysaccharide acting through the CD14 molecule. Eleven SBS and 10 age- and BMI-matched control subjects were included into the study. The effect of parenteral nutrition was assessed after 14 days, 6 and 12 months from its initiation, respectively. At baseline, SBS patients had increased gut permeability as measured by zonulin (47.24±2.14 vs. 39.48±1.20 ng/ml, p=0.006) and LBP (30.32±13.25 vs. 9.77±0.71 µg/ml, p<0.001) compared to healthy controls. Furthermore, SBS subjects had reduced FABP-2, unchanged citrulline and increased sCD14 and GLP-2 relative to control group. Throughout the whole study period the administered parenteral nutrition had no significant effect on any of the studied parameters. Taken together, our data show that patients with short bowel syndrome have increased intestinal permeability that is not affected by parenteral nutrition.