Rhabdomyosarcomas (RMS) of the urinary bladder and vagina vary in their biologic and clinical behavior and require different types of treatment. Anatomically the two organs are close, and the reason for these differences in behavior is unknown. We investigated tumor specimens of 51 urinary bladder RMS and 14 vaginal RMS with regard to histologic subtype, growth pattern, differentiation, and proliferation morphologically and immunohistochemically. Recurrences and/or "second look" specimens from 15 patients after chemotherapy were compared with the primary tumors. Within the 65 specimens we found 31 "classical" embryonal RMS, 26 embryonal RMS of botryoid subtype (BRMS), 3 embryonal RMS of spindle cell subtype, and 5 alveolar RMS. BRMS is more common in the vagina (11 BRMS of 14 cases) than in the urinary bladder RMS (15 BRMS of 54 cases). Classical embryonal RMS with a polypoid (exophytic) growth pattern is associated with a more favorable prognosis (92% 10-year survival) than the same type with a diffuse intramural (endophytic) growth pattern (68% 10-year survival, p = 0.02). The proliferation rate was associated with the degree of differentiation, but neither showed a correlation with prognosis. A marked maturation after chemotherapy was seen in the majority of recurrences and SL specimens, associated with lowered proliferation activity. Two of 12 patients with recurrences showing chemotherapy-induced maturation died of the disease. In conclusion, we determined that polypoid embryonal RMS of both the urinary bladder and the vagina have a comparably good prognosis. This includes all botryoid RMS. The poorer prognosis of the group of urinary bladder RMS as a whole was caused by a high incidence of diffusely growing RMS, which have a less favorable prognosis than polypoid RMS. Maturation after chemotherapy occurs frequently in RMS. In contrast to the excellent prognosis reported in other studies, we had two patients with fatal outcome despite chemotherapy-induced maturation in the recurrences.