The first case of Q fever in Taiwan was reported in 1993. The disease is considered to be emerging in Taiwan, but the route of transmission has remained unclear. The annual number of confirmed Q fever cases has been increasing up to more than 100 cases since 2005, comparing with less than 30 before 2003. The purpose of this study was to determine the seroprevalence and risk factors of Coxiella burnetii infection in veterinary-associated populations in southern Taiwan. A total of 228 serum samples of high risk individuals engaging in veterinary-related work or animal-farm work, were collected between March and June in 2007. The study individuals were interviewed by a structured questionnaire designed for Q fever investigation. Serum samples from different animal species were also obtained for Q fever analysis in the same study areas. Serological test was conducted by indirect immunofluorescence antibody assay (IFA). The result demonstrated the overall seroprevalence of Q fever was 26.3% in individuals engaging in veterinary and animal-related work in southern Taiwan. After multiple logistic regression analysis, goat exposure was significantly associated with seropositivity of Q fever in the study population in southern Taiwan (adjusted odds ratio: 2.62; 95% CI: 1.06–6.46). In addition, the highest seroprevalence (43.8%) of Q fever was identified in goats (P < 0.05). Finally, this study documented that people with prior knowledge of Q fever were less likely to be seropositive for C. burnetii. It was concluded that goat exposure was the most important risk factor associated with C. burnetii infection and appropriate health education could be useful to prevent high risk individuals from the infection in southern Taiwan.