In Japan, chemotherapy for urogenital malignant diseases is commonly performed by urologists and febrile neutropenia (FN) is one of the major adverse events associated with chemotherapy, however, few reports exist from the urological field about FN. In this present study, a total of 883 courses of chemotherapy (326 patients) performed from 2010 to 2011 at 10 University Hospitals were retrospectively reviewed. The regimens were GC (gemcitabine and cisplatin), GCP (gemcitabine, cisplatin and paclitaxel) and M-VAC (methotrexate, vinblastine, doxorubicin, cisplatin) for urothelial carcinoma, and EP (etoposide and cisplatin) and BEP (bleomycin, etoposide and cisplatin) for testicular cancer. In 81 courses (9.2%, 66 patients; 20.2%) including FN, antimicrobials and granulocyte-colony stimulating factor (G-CSF) were administered in 69 courses (85.2%) and in 77 courses (95.1%), respectively. The MASCC risk-index score was evaluated in no more than 51 courses (63.0%) and 1 patient with 18 points on the MASCC score died due to myelotoxicity and infections. According to statistical investigations, FN is significantly more frequent in GCP and M-VAC than in GC (p = 0.0073, <0.0001) and in a sim