Endoscopy plays a pivotal role in diagnosing gastrointestinal (GI) symptoms of pediatric patients post hematopoietic stem cell transplantation (HSCT). There is very little data on whether endoscopic findings can predict pathological diagnosis and treatment outcomes in the pediatric population. The primary objective was to determine the association between macroscopic and microscopic findings of endoscopies in pediatric patients post-HSCT. A secondary objective was to evaluate whether macroscopic findings can predict treatment outcomes or differentiate between causes of GI symptoms. This single-center prospective study analyzed the results of endoscopic evaluation in patients aged 18 years or younger, who developed GI symptoms during and after HSCT and required an endoscopy for diagnosis. Macroscopic and microscopic findings of upper and lower endoscopies were reviewed and compared, thus evaluating the correlation between the two. Predetermined sites throughout the GI tract were examined for their macroscopic and microscopic findings, to examine whether their results suggest graft-versus-host disease (GVHD), infection, or both. Patients' change in treatment and clinical response were also assessed. In 22 patients, 249 tissue samples were macroscopically and microscopically evaluated. When abnormal macroscopic findings were present, microscopic findings were present in 86.2% of the cases. In 72.1% of the endoscopic sites with normal macroscopic results, abnormal microscopic findings were present (p value = 0.004, Fisher-Freeman-Halton exact test). This study provides further evidence supporting the correlation between macroscopic and microscopic evaluation in the diagnosis of GVHD post-HSCT, however, normal macroscopic findings do not rule out the presence of GVHD.