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Patients with Crohn’s disease (CD) face malnutrition risk, which, combined with inflammation, can lead to sarcopenia, associated with a worse prognosis. The purpose of the present study was to assess malnutrition and sarcopenia in patients with CD. Fifty-three patients (26 women) participated (38.1 ± 10.9 years, 79% in remission). Body composition, physical performance, nutritional questionnaires, and biomarkers were performed. Malnutrition was screened with the Mini Nutritional Assessment (MNA) and the Malnutrition Inflammation Risk Tool (MIRT) and was assessed with the Global Leadership Initiative on Malnutrition (GLIM) tool using etiologic along with three different phenotypic criteria: low Body Mass Index (BMI), low Calf Circumference (CC), and low Fat-Free Mass Index (FFMI). To find cases and evaluate sarcopenia, the Sarcopenia Questionnaire (SARC-F) and European Working Group on Sarcopenia2 (EWGSOP2) criteria were used. Malnutrition rates were 11.3% (n = 6), 7.5% (n = 4), and 5.6% (n = 3) based on low FFMI, CC, and BMI, correspondingly. Four (7%) patients had low Hand-Grip Strength (HGS), n = 8 (14.8%) had low Appendicular Lean Mass (ALM), and n = 3 (5.6%) had low gait speed. No-one had sarcopenia. A high albumin and triceps skinfold pattern, identified by principal component analysis, was related to reduced C-Reactive Protein (CRP) levels (B = −0.180, SE = 0.085, p = 0.045). In conclusion, based on the studied anthropometric, nutritional, and functional variables, CD patients were not diagnosed with sarcopenia in the present study. Body composition patterns were related to the inflammatory burden …