Primary sarcomas of the bladder and prostate are exceedingly rare, often highly aggressive and account for less than 1 % of all malignant tumors of these organs. In this landscape study, we searched for genomic biomarkers that could aid in either treatment selection or further classification of these tumors. 18 (0.2 %) bladder sarcomas were identified from 11,193 bladder cancers and 11 (0.6 %) prostate sarcomas were identified from 19,057 prostate cancers that underwent hybrid capture-based comprehensive genomic profiling (CGP) to assess all classes of genomic alterations (GA). The bladder sarcomas included 12 leiomyosarcomas, 3 rhabdomyosarcomas and 3 high-grade undifferentiated sarcomas. The sarcomas of the prostate featured 9 primary prostatic stromal sarcomas, 1 leiomyosarcoma and 1 rhabdomyosarcoma. The most frequent gene alterations were in TP53, RB1 and ATRX. Bladder sarcomas were also found to have more than 2-fold more genetic alterations than compared to prostatic sarcomas.