This study was designed to investigate the impact of haematopoietic stem cell transplantation (HSCT) on Helicobacter pylori colonization of the oral mucosa by nested polymerase chain reaction (nested-PCR). Forty six consecutive patients submitted to HSCT and 46 healthy volunteers were included in the study. Oral swabs were taken from the oral mucosa of the patients and control group. The medical records of the patients were reviewed and the following information was retrieved: gender and age of the patient, donor gender, primary disease, stem cell source (bone marrow or blood stem cells), leukocyte, neutrophil and platelet counts, and chronic graft versus host disease (cGVHD) of salivary glands. The results demonstrated an increased frequency of H. pylori in the oral mucosa of HSCT patients compared to controls (rho = 0.002). The presence of H. pylori in the oral mucosa was not related to the severity of cGVHD. The median counts of platelet/mm3, leukocytes/mm3 and neutrophils/mm3 in the group of HSCT patients positive for H. pylori were not statistically different from those of the patients negative for it. In conclusion, the present study shows increased frequency of H. pylori in the oral mucosa of HSCT patients compared to non-transplanted healthy volunteers.