Crohn’s disease (CD) is a chronic inflammatory transmural disease of the gastrointestinal tract. The small bowel is the most frequently involved site. Assessment of the bowel is essential in guiding therapeutic decisions, medical or surgical therapy. Personalized medicine is a new concept that has the potential to improve therapeutic efficacy, reduce the risk of drug adverse events, and decrease costs if the therapy is the most suitable treatment for selected patients. Many techniques have been verified and standardised for small bowel CD. Among radiological techniques, CT enterography (CTE) and MRI-enterography (MRE) are the most widely accepted techniques, although MRI is generally preferable as it avoids radiation. In this review, we will present the current role and new innovative technological perspectives of MR enterography in comparison with clinical and endoscopic evaluations for the assessment of CD activity in adult patients. In particular, many studies have been performed to validate MRE signs such as biomarkers of active Crohn’s disease (such as mural thickening, mural T2 hyperintense signal, target sign, comb sign, ulceration and extramural mesenteric signs) and to select the most appropriate index for identifying active disease or severe inflammation (such as MaRIA score, Clermont index, and others). We conclude that MRE is a minimally invasive tool for the evaluation of disease activity and shows a very good correlation with the presence and severity of endoscopic lesions, so to allow a personalized medicine in patients with CD.