: Growth failure and malnutrition are major concerns in pediatric patients with frequent relapses of Crohn's disease (CD). In search of an early, noninvasive marker of relapse, we prospectively examined the relationship between levels of fecal α1-antitrypsin (α1-AT) in comparison with other known inflammatory parameters and disease activity using a pediatric CD Activity Index (P-CDAI), as well as in relation to growth. Forty-two pediatric patients (29 M, 13 F, 7-16 years old, mean 12.8 years) with ileal or ileocolonic CD were prospectively examined at 4 monthly intervals over a 1 year period. Median (interquartile range) fecal α1-AT values did not differ between children in clinical relapse (P-CDAI > 150, n = 10) compared with CD patients (n = 42) with quiescent disease [1.84 (3.67) mg/g versus 1.55 (3.97) mg/g, respectively, p = ns]. However, children with growth failure (n = 14) had a significantly higher fecal α1-AT [3.63 (5.65) mg/g] despite clinical remission [median P-CDAI 22 (72.5)] compared with those with normal growth [1.41 (1.66) mg/g, p = 0.02]. Very high fecal α1-AT levels (>4 mg/g) were not associated with clinically active disease [median P-CDAI 23 (71.5)]. Overall however, levels in CD were significantly higher than that of 17 pediatric control patients with diarrheal disorders unrelated to IBD [0.98 (1.21), p < 0.05]. Fecal α1-AT seems therefore not to be a reliable marker of clinically evident disease activity, but was best correlated with chronic malnutrition and subclinical disease activity.