The long-term cryopreservation of the germplasm (spermatozoa and oocytes) of threatened species offers flexibility in their genetic management and security against disasters or outbreaks of disease that might seriously affect subpopulations. A wide range of infectious diseases can, however, be transmitted via artificial insemination, and the risk of infectious diseases being spread via manipulated germplasm needs to be carefully managed in order to avoid fertility problems in the dams and decreased survival of offspring. Furthermore, accidental introduction of exotic microorganisms into ecosystems remain a major threat. The aims of the present study were to assess the impact of diseases transmissible by sperm on the establishment of germplasm banks for the Iberian ibex, a wild mountain ungulate, and to determine the influence of the presence of these pathogens on sperm functionality. Blood and sperm samples were obtained from 52 mature ibex males legally shot in southern Spain. Sperm motility, morphological abnormalities, acrosome integrity and plasma membrane integrity were assessed for each sample to determine in vitro sperm quality. All serum samples underwent serological analysis for bovine herpes virus type I, bluetongue virus (BTV), bovine leukaemia virus, caprine arthritis-encephalitis virus, pestivirus, Brucella, Coxiella burnetii, Chlamydiophila abortus, Mycoplasma agalactiae and Borrelia burgdorferi. The highest prevalence (30.7%) was recorded for B. burgdorferi, followed by C. burnetii (13.4%). A total of 734 sperm doses containing approximately 200× 10 6 spermatozoa each were frozen in straws. Forty-five straws (6.1% of the total number) came from animals seropositive for diseases listed in the Terrestrial Animal Code of the OIE for collection and processing of bovine and small ruminant semen (in this case, pestivirus and BTV). A total of 271 frozen straws (36.9% of the total of frozen straws) were provided by animals seropositive for pathogens potentially transmissible by semen not included in the above OIE code (in this case, B. burgdorferi and C. burnetii). The values of sperm variables were not affected by seropositivity for any of the pathogens transmissible by sperm.