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Introduction: Mucosal Healing (MH) is becoming an increasing tool in the management of patients affected by inflammatory bowel diseases and is set as the endpoint of a therapy in clinical trials, especially for the recently introduced biological agents. MH is evaluated by direct investigation instruments and in most clinical trials these are represented by endoscopy. There is no definition of MH in pathology and there are no established evaluation criteria of MH among pathologists. Aim of this study is to find a pathological definition of MH and a pathological score as useful as endoscopy scores to the clinical management. Methods: a population of 51 patients in pediatric age is selected, affected by both Crohn’s disease and ulcerative colitis, and is treated for 1 year with Azathioprine. All patients undergo colonoscopy with biopsies at the beginning and at the end of the therapy. Patients are followed for 2 years after the end of the trial and some of them have biopsy follow up. Biopsies are evaluated with two different scores, the Combined Architectural and Inflammatory Score and the Activity Score in order to evaluate MH. An immunohistochemical analysis is also performed. Results are correlated with Endoscopy and follow up. Conclusions: Among the two scores, the Activity Score exhibited higher correlation with endoscopy, demonstrating the usefulness of pathological MH. Moreover, both scores produced a significant prediction of release during follow up.