Malnutrition is common in patients with Crohn’s disease and negatively influences immunity and quality of life. The optimal tools for nutrition assessment in patients with Crohn’s disease are not clearly defined and lead to variations in practice. With this review, we aimed to appraise the existing evidence for nutrition assessment of patients with Crohn’s disease compared with healthy controls and provide a comprehensive guide with relevant measures applicable to clinical practice. A literature search using Medline, Embase, and Scopus from inception to October 1, 2018, was conducted.