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A cross-sectional epidemiologic investigation was undertaken to identify tick-borne pathogens in Mongolian livestock across two provinces (aimags) from 2007 to 2008. Serology and PCR were used to identify exposure to and infection with Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, A. ovis, and spotted fever group rickettsiae species in the animals sampled. Factors evaluated for association with pathogen prevalence included region, body condition score, gender, and species. Khuvsgul livestock had high seroprevalence to A. phagocytophilum (64%), and A. ovis (77%); Khenti livestock had a high exposure to spotted fever group rickettsiae species (48%). Females and intact males had higher prevalence to A. phagocytophilumthan castrated males, as did small ruminants compared to cattle and horses. Animals with lower BCS, or animals living at higher elevations, had a greater prevalence odds of exposure to pathogens for spotted fever group rickettsiae and A. ovis, respectively. Reports of the newly identified Rickettsia and Borrelia species in the neighbouring provinces of northern China combined with the data from this study warrant further investigation of tick-borne pathogens to identify reservoir hosts and infection in Mongolian herders.