Purpose: We aimed to elucidate the relationship between plasma free amino acid profiles and changes in the Crohn’s disease activity index (CDAI) among patients with Crohn’s disease (CD) after administration of an elemental diet (ED). Patients and methods: We measured fasting plasma concentrations of free amino acids in 5 patients with CD and evaluated the relationship between amino acid concentration and disease activity at 4 weeks after administration of an ED. Results: Concentrations of valine, lysine, tyrosine, and glutamic acid were significantly increased after administration of an ED. Significant correlations were noted between changes in CDAI scores and valine concentrations. Tryptophan concentrations also exhibited a strong correlation with CDAI scores. Conclusion: In patients with CD, plasma concentrations of valine and tryptophan appear to be associated with disease activity following treatment with an ED.