Mucositis is a common and vexing complication of autologous progenitor cell transplantation (ABMT). A modified oral mucositis assessment scale (OMAS) has been found to be a reproducible and effective tool for monitoring mucositis after radiation therapy or chemotherapy. We utilized the modified OMAS scale to study clinical parameters associated with the development of mucositis in 79 patients undergoing ABMT. Median patient age was 52; 61% had non-Hodgkin's lymphoma (NHL), 23% multiple myeloma and 14% Hodgkin's disease. Patients were mobilized with G-CSF alone or the combination of etoposide plus G-CSF. Univariable correlates of worse mucositis were prior radiation therapy (P = 0.004), a diagnosis of NHL (P = 0.014), progenitor cell mobilizing regimen containing etoposide (P = 0.001), and ABMT preparative regimen containing etoposide (P = 0.006). Multivariable regression analysis revealed that NHL diagnosis (P = 0.007), prior radiation therapy (P = 0.001), and etoposide in the mobilizing regimen (P = 0.034) were associated with worse post-transplant mucositis. Worsening mucositis correlated with a longer inpatient length of stay. We conclude that several variables contribute to worsening mucositis during autologous transplantation, including etoposide in the progenitor cell mobilizing regimen.