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This study investigated the prevalence of zoonotic pathogens in stray dogs including toxoplasmosis, heartworm disease, Lyme disease, leptospirosis and Q fever in central Taiwan (Taichung, Changhua and Yunlin County) using nested, semi-nested or traditional polymerase chain reaction. Associations between prevalence of the infections and demiographic data of stray dogs in central Taiwan were also analyzed. Blood samples were randomly collected from stray dogs every month from August 2009 to July 2011. Total DNA extracted from blood samples ranged from 0.8 to 1.5 μg as the sensitivity of PCR ranged from 10 fg to 100 pg. For the PCR primers no cross-reaction was found between the nucleic acids of interest and DNA extracted from Ehrlichia cani, Babesia canis and Babesia gibsoni. The prevalence rates of 5 zoonotic diseases in the stray dogs were as follow: Toxoplasma gondii 3.89 % (28/720), Dirofilaria immitis 7.22% (52/720), Borrelia burgdorferi 5.42% (39/720), Leptospira spp. 7.22% (52/720), and Coxiella burnetii 5.83% (42/720). The association analysis between the prevalence rates and epidemiological data of stray dogs as well as sampling season showed that the prevalence rates of Toxoplasma gondii, Borrelia burgdorferi, and Leptospira spp. were correlated with the age and season but not with breed and gender. The prevalence rate of Dirofilaria immitis species was associated with breed and the season but not with gender and age while the prevalence rate of Coxiella burnetii was linked with the season but not with breed, gender and age. Our study reveals the prevalence of toxoplasmosis, heartworm disease, Lyme disease, leptospirosis and Q fever in stray dogs in Taiwan and provides crucial information for prevention and control of zoonotic diseases in Taiwan and neighboring areas and countries. [ABSTRACT FROM AUTHOR]