Patients undergoing allogeneic stem cell transplantation are at high risk for infection with a variety of pathogens during different phases of the procedure. Human infections due to Bartonella spp. are viewed as emerging diseases typical in, although not exclusive to, immunosuppressed patients, in particular those with AIDS, organ transplants and haematological malignancies. We describe four patients, three children and one adult, who developed vegetating papillomatous lesions exclusively on the oral mucosae. They shared a history of haematological malignancy and allogeneic bone marrow/stem cell transplantation, and later developed chronic graft-versus-host disease, also involving the oral mucosae. Histopathologically, the vegetating lesions were characterized by a diffuse neoangiogenesis, granulation-like tissue, and a mixed cell infiltrate predominantly composed of neutrophils. Gram-negative bacteria were found in the endothelial cells of the vessels in the deeper portion of the corium by electron microscopy. In three cases, DNA of B. henselae was detected by polymerase chain reaction (PCR), and confirmed by sequencing of the PCR products. All the lesions healed after systemic antibiotic therapy, although some recurred after months, and regressed again after systemic antibiotic treatment associated with conservative surgical excision.