Recent research has shown that cancer patients undergoing bone marrow transplantation (BMT) experience moderate to severe mouth pain due to treatment-related mucositis in spite of morphine therapy. Treatment-related emotional distress in BMT patients is also described widely. This study examined several biomedical, psychological and social variables as possible predictors for the intensity of treatment-related mouth pain and anxious mood in 63 cancer patients undergoing BMT or stem cell transplantation (SCT) within a prospective longitudinal design. Biomedical predictors included biomedical risk, mucositis, the mode of transplantation, total body irradiation, age and gender. Psychological predictors were depression (BDI), BMT-related distress, chronic stress and resources in everyday life (KISS), pain-related coping behaviour (KPI-17) and social support (ISSS). Among the social variables we evaluated education, being married and the living situation. Criteria variables were the intensity of mouth pain and anxious mood which were assessed daily by numeric self-rating scales for 24 days after transplantation. Results of stepwise multiple regressions indicated that psychological and social variables were important predictors of mouth pain, besides biomedical variables. Whereas the biomedical variables revealed the most predictive power during the second week after BMT, psychological predictors were more important during the early and late phases of the treatment. Daily anxious mood was best predicted by psychological and social variables. Among the biomedical variables mucositis was most strongly related to mouth pain besides mode of transplantation, risk, TBI and age. Among the psychological variables BMT-related distress was the most important predictor, with resources in private life or at work and pain-related coping modes as further significant predictors. These results imply that relevant predictors should be assessed as high risk factors for an increased vulnerability for treatment-related side-effects before treatment starts indicating an additional offer of psychological treatment in high risk patients.