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Fecal calprotectin and lactoferrin are promising noninvasive biomarkers for intestinal inflammation. In Crohn's disease (CD), during anti-TNF-alpha (TNF-α) treatment, the clinical significance of these markers has, however, been insufficiently explored.Among CD patients receiving anti-TNF-α therapy we assessed the role of fecal calprotectin and lactoferrin as surrogate markers for mucosal healing. Before and 3 months after the beginning of anti-TNF-α induction, 15 patients underwent ileocolonoscopy with scoring of the Crohn's Disease Index of Severity (CDEIS). Fecal samples for calprotectin and for lactoferrin measurements were collected and the Crohn's Disease Activity Index (CDAI) was calculated at the time of the endoscopies and 2 and 8 weeks after the first treatment.The median CDEIS fell from 13.0 to 4.8 (P = 0.002) and CDAI from 158 to 68 (P = 0.005). Accordingly, the median fecal calprotectin concentration fell from 1173 μg/g to 130 μg/g (P = 0.001) and fecal lactoferrin from 105.0 μg/g to 2.7 μg/g (P = 0.001). Of the 15 patients, 11 (73%) showed an endoscopic response to treatment and 5 of these achieved endoscopic remission (CDEIS < 3). In those 5 patients the fecal calprotectin concentration declined from 1891 μg/g (range 813–2434) to 27 μg/g (13–130) and lactoferrin from 92.4 μg/g (35.5–235.6) to 1.9 μg/g (0.0–2.1).Compared to pretreatment values, concentrations of fecal calprotectin and lactoferrin after the anti-TNF-α treatment were significantly lower. During anti-TNF-α therapy these fecal neutrophil-derived proteins may thus be useful surrogate markers for mucosal healing.