The present study was aimed to investigate the prevalence of some protozoa (B. caballi, T. equi, T. gondii, Neospora sp.) and viral agents (equine influenza, equine viral arteritis, equine herpesviruses) of equids in Balikesir and its surroundings, in Turkey. Plasma and serum samples were collected from 66 horses and 96 donkeys. Babesia caballi, T. equi, Neospora sp. antibodies were detected with c-ELISA while T. gondii antibodies with the Sabin Feldman Dye test. Viral agents were detected by using the PCR technique. The prevalence rates of the protozoa in horses were 12.12% for B. caballi, 34.84% for T. equi, 9.09% for T. gondii, and 10.6% for Neospora sp. respectively. The molecular prevalence of the viral agents was detected as 3.03% for equine influenza virus, and 6.06% for equine herpesvirus 5. Equine viral arteritis virus and other herpesviruses (1,2 and 4) were not detected (0%) in any of the samples. However, the rates of seropositivities in donkeys were B. caballi 1.69%, T. equi 71.87%, T. gondii 90.62%, Neospora sp. 23.95%, equine influenza virus 1.04%, equine viral arteritis virus 0%, equine herpesvirus-5 3.12%, and other herpesviruses 0%. The results indicated that T. equi was more prevalent than B. caballi in both species. This study is important about being is the first study in Turkey that reported the existence of anti-Neospora sp. antibodies in donkeys, and the seroprevalence of T. gondii west side of the country in horses and donkeys.