After having been informed about current guidelines, all urologic units in hospitals and private practices in Frankfurt/Main were visited in 2005/6 by members of the public health department and assessed using a checklist based on the recommendations of the German Guidelines for reprocessing medical instruments including rigid and flexible cystoscopes. In 12 hospitals and 22 private practices cystoscopy was performed using rigid cystoscopes, whereas flexible cystoscopes were used in 7 hospitals and 8 private practices. Cystoscopy with flexible instruments was more common in ambulatory than in clinic settings (about 1150/year vs. 280/year). In hospitals, reprocessing of the rigid cystoscopes was performed in special units for reprocessing (disinfection, sterilisation) using validated automatic processes, whereas reprocessing of flexible cystoscopes often was performed in the urologic units themselves, and not always in a correct manner. In the private practices, mainly manual reprocessing procedures were in use for rigid cystoscopes, in 18 out of 22 practices correct. However, only in 50 % of the private practices, sterilisation equipment was available for reprocessing rigid cystoscopes and/or endoscopic accessories. Flexible cystoscopes were reprocessed using a washer-disinfector in one practice, in the other ones, manual reprocessing was performed. In two practices only, reprocessing according to the guidelines was seen. Infection control advice and repeated control of the public health department resulted in the correction of most processing faults within some months.