High-dose chemotherapy with autologous stem cell transplantation (ASCT) is increasingly utilized in patients with relapsed and refractory germ cell tumors (GCT). Infectious complications are common after ASCT for hematologic malignancies, but their epidemiology in GCT patients has not been described. To identify infectious complications of ASCT for GCT, we conducted a retrospective study of patients treated at our institution, a tertiary-care cancer center in New York City between 1994 and 2006. Patients received ciprofloxacin prophylaxis but no routine antifungal or antiviral prophylaxis. In addition, patients were housed in shared rooms of 2 with standard precautions during hospitalizations. Overall, 107 patients with relapsed or refractory GCT were treated with 1-2 cycles of paclitaxel/ifosfamide and 1-3 cycles of high-dose carboplatin/etoposide with ASCT. Sixty (56%) of 107 patients developed 95 total infections, including 33 catheter-associated bloodstream infections. Fungal, viral, and nosocomial infections were uncommon. There were no infection-related deaths. In conclusion, serious morbidity from infection is uncommon among GCT patients receiving high-dose chemotherapy with ASCT. Isolation and aggressive antifungal and antiviral prophylaxis is not warranted in these patients.