Non-invasive markers able to identify patients with chronic diarrhea at risk of organic disease are missing. Aim of the study was to assess the diagnostic ability of intestinal permeability (IP) test and fecal lactoferrin (FL) in distinguishing functional from organic disease in patients with chronic diarrhea. We retrospectively enrolled patients referring to the gastroenterology outpatient clinic for chronic diarrhea. Among the 103 patients included, 40 % had an organic disease, with IP and FL levels significantly higher compared to those with a functional disorder (p < 0.0001). Sensitivity, specificity, positive and negative likelihood ratios, area under ROC curves of FL were superior to those of IP in discriminating functional and organic disease (FL: 87.8 and 93.6 %, 13.61 and 0.13, 0.9375; IP: 61.0 and 90.3 %, 6.3 and 0.43, 0.7691). When combining the two tests, the diagnostic ability of FL did not improve. In subgroup analysis, IP confirmed its ability to detect small bowel alterations, while FL could identify both small bowel and colonic alterations. In conclusion, FL is valid to detect inflammation in the gastrointestinal tract, while IP can effectively identify small bowel damage in chronic diarrhea patients. Together these tests could recognize both the presence of intestinal damage and its site.