Rodents play an active role in the transmission of a number of zoonoses by harboring and disseminating the pathogens involved, either through their biological materials or via their ectoparasites. Hence, the spatial and seasonal distribution of potential agents of zoonoses may be studied by examining their distribution in the rodent vectors and their ectoparasites. A surveillance was conducted in wild rodents in 51 different areas of Cyprus, an island ecosystem, to monitor the reemergence of Echinococcus granulosus and Encephalomyocarditis virus (pathogens that have been eradicated from Cyprus), to study the presence and dispersal of Salmonella spp. (a bacterium found in patients and poultry in the island), as well as to investigate the presence of helminth parasites and rodent ectoparasites. Biological material collected from 625 rodents, examined macroscopically, microscopically, and after culture, showed that the most widespread pathogens encountered in wild rats (Rattus rattus and Rattus norvegicus) were helminth parasites, found in 92 animals (three helminth species found for the first time in Cyprus: Cysticercus fasciolaris, Hymenolepis diminuta, and Physalloptera spp.), and Salmonella spp., detected in the intestine of 56 rats (12 different Salmonella spp. and serotypes). None of the rodents were found infected with the cestode Echinococcus or Encephalomyocarditis virus, indicating that the control measures taken by the Veterinary Services on the island prevented its reestablishment despite changing conditions. The rodents were also free of the nematode Trichinella. Over 40% of the rats collected were infested with fleas, mainly Xenopsylla cheopis. The results, analyzed using the Geographical Information System technology, revealed two of the areas studied as high risk for public health.