Bacterial contamination of peripheral blood hematopoietic cells collected for autologous bone marrow transplantation occurs sporadically. Although transfusion of contaminated hematopoietic cells without adverse clinical sequelae has been reported, detailed guidelines for transfusing cells with contamination are not available. We report a case of autologous hematopoietic cell transplantation that necessitated using multiple aliquots of peripheral blood hematopoietic cells known to be contaminated with coagulase-negative Staphylococcus bacteria. Prophylactic intravenous antibiotic therapy was given with the infusion of contaminated hematopoietic cells. The patient had positive results on a blood culture, but engraftment was successful, and serious adverse effects did not occur. With appropriate microbial identification and prophylactic antibiotic therapy, contaminated hematopoietic products can be safely infused when necessary with a good clinical outcome.