Graft-versus-host disease (GvHD) is a complication of hematopoietic cell transplantation, and the small bowel is one of the main targets in the gastrointestinal tract. Capsule endoscopy is a safe procedure and can be useful in the diagnosis of GvHD. The aim of the present study was to compare the diagnostic yield of capsule endoscopy with the histopathologic findings in GvHD. A retrospective diagnostic test study included all the patients with suspected GvHD that underwent gastroscopy and colonoscopy, with histopathologic evaluation of the biopsies taken, and capsule endoscopy, within the time frame of July 2015 and July 2019. Capsule endoscopy findings were compared with the histopathologic diagnosis, considered the gold standard. Twenty-one patients with GvHD (7 [33%] women; 37±11.9 years of age) were included, 20 (95%) of whom had acute GvHD. The median gastric transit time of the capsule was 55minutes (20-113) and the median small bowel transit time was 261minutes (238-434). The entire small bowel was visualized through capsule endoscopy in 17 cases (80.95%). The histopathologic findings and capsule endoscopy findings resulted in the diagnosis of GvHD in 17 and 16 cases, respectively. There was agreement between the histopathologic and capsule endoscopy findings in 18 cases (15 positive and 3 negative). Sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic yield of capsule endoscopy were 88%, 75%, 94%, 60%, and 85%, respectively. Capsule endoscopy is a safe tool for the diagnosis of GvHD, with high sensitivity and positive predictive value, as well as moderate agreement with histopathologic findings.