Nowadays Gram-positive cocci, especially oral viridans streptococci (OVS) and coagulase-negative staphylococci (CoNS), are the most common bloodstream isolates in febrile neutropenic patients. Although in general these cocci are quite indolent, Streptococcus mitis is associated with serious complications such as sepsis and/or adult respiratory distress syndrome. Neutropenia is the most significant predisposing factor but the impact of mucositis, i.e. damage to the mucosal barrier of mouth and intestines (mucosal barrier injury, MBI), is very much greatly underestimated. Oral mucositis is a strong predictor of OVS bacteremia and simultaneously CoNS bacteremia is clearly associated with mucositis. Treatment with especially high dose cytarabine, cyclophosphamide and idarubicin, when given to allogeneic hematopoietic stem cell transplant recipients, predictably results in mucositis. Hence, the occurrence of mucositis should have implications for complementing empirical therapy with specific drugs such as glycopeptides, because risk patients can be selected based upon the chemotherapeutic therapy administered. An algorithm is presented for dealing with patients at high risk of mucositis and bacteremia due to Gram-positive cocci.