ABSTRACT Introduction: Acute graft-versus-host disease (GVHD) is one of the major causes of morbidity and mortality in patients undergoing allogeneic hematopoietic stem cell transplantation (AHSCT) and has become the subject of several studies to understand and treat it. Objective: This study does a descriptive analysis of the apoptotic index (AI) evaluation and intestinal permeability (IP) alterations in association with the clinical, endoscopic and histopathological data on patients undergoing AHSCT, with emphasis on acute intestinal graft-versus-host disease (GVHD) diagnosis. Methods: Thirty-one patients were divided into two groups—one of patients with a clinical GVHD diagnosis and one of those without GVHD diagnosis. Results: Thirteen deaths (41.9%) occurred during the study period, thereby reaffirming the severity of the alterations found in the patients. Fifteen patients subjected to 21 esophagogastroduodenoscopy procedures prior to D + 90 post-transplant had visible endoscopic alterations and 19 biopsies revealed histological alterations to the stomach and duodenum. Higher apoptotic indices, not reaching statistical significance, were observed in patients who died of graft versus host disease (GVHD), in the more acute forms of GVHD and where clinical GVHD was present. The intestinal permeability evaluation was performed on nine patients able to undergo it in the three proposed study periods, which showed alterations, some of which were pronounced even during pre-transplant and, therefore, the pre-conditioning phase. Conclusion: Clinical judgment remains a fundamental tool in the diagnosis of GVHD. This study points to the known limitations of traditional diagnostic aids (endoscopy and histology) and points to new methods not usually employed in clinical practice.