Pneumocystis carinii pneumonia (PCP) is uncommon in patients undergoing chemotherapy for breast cancer. Most previously described patients with breast cancer and PCP received treatment with corticosteroids, a known risk factor for PCP. We describe two patients with metastatic breast cancer who developed PCP after receiving therapy with high doses of cyclophosphamide with peripheral blood stem cell support. Both patients developed fevers of unclear etiology in the setting of recovery of the neutrophil count. Only one patient had pulmonary symptoms. P. carinii infection was documented in both cases by bronchoscopy. One patient died after prolonged ventilatory support for PCP. Steroid exposure did not appear to be a risk factor for the development of PCP in either patient. Patients receiving sequential high doses of chemotherapy with stem cell support may be at increased risk for PCP. The role of prophylaxis for PCP in this setting should be continually redefined as the type and intensity of chemotherapy, as well as methods of procurement of autologous stem cells, continue to change.