The prevalence of Coxiella burnetii in native Korean goats in Jeonbuk province was investigated using ELISA (sera) and PCR (vaginal mucus). A total of 798 blood samples from 189 farms were collected in 2013 and 2015. Sero-prevalence was 13.6% in 2013 and 15.7% in 2015. Tracking survey of six seropositive farms on the prevalence of C. burnetii was conducted. 137 (41.4%) out of 331 goats were seropositive and 47 (17.6%) out of 267 goats were positive in PCR. The higher seropositivity observed in adult goats and female goats significantly, the seroprevalence of C. burnetii was higher as age increased (＜1 y=13.2%∼≥5 y=100%)(P＜0.05) and female goats (44.8%) was higher than male goats (24.1%) on the seroprevalence (P＜0.05). 21 (7.9%) goats positive in PCR was seronegative. The prevalence of C. burnetii in native Korean goats in slaughter house was 30.0% in ELISA and 11.5% in PCR. Significantly, female goats (62.8%) was higher than male goats (12.3%) on the seroprevalence (P＜0.05). Based on these data, C. burnetii was easily exposed in domestic animals: native Korean goats-related areas such as farms and slaughter house.