The present study was performed to determine the prevalence of Coxiella burnetii in goat milk and serum samples collected from the Lorestan province. A total of 200 milk samples and 200 serum samples were randomly collected from goat herds belonging to four different geographical areas of Lorestan province. Milk and serum samples were collected during 1399 and, the age of the animals was recorded. DNA was extracted from all milk and serum samples. Then Nested-PCR was used to detect Coxiella burnetii based on the gene responsible for encoding a bacterial outer membrane protein (Com1) weighing 27 kDa. A 438 bp fragment of the Com1 gene was amplified. The results showed that out of 400 milk and serum samples, 34 samples (17%) were positive for Coxiella burnetii infection. Also, out of 200 milk samples, 26 samples (13%), and out of 200 serum samples, eight samples (4%) were infected with Coxiella burnetii. There was a significant difference (p <0.05) in the excretion of Coxiella burnetii through milk, based on season, geographical area, and age groups, but there was no significant difference between infected sera. Bacterial excretion in milk was very common in summer based on the season (21 samples (39.5%) and also the highest level of infection based on the geographical area in the east (14 samples (27.5%)) and based on age groups in the group. Age over 7 years (16 specimens (21%)) was observed. Conclusion Due to the importance of Coxiella burnetii, its rapid and accurate diagnosis is very important. Nested-PCR molecular technique can be very effective due to its high accuracy, sensitivity, and high speed in the detection process. Therefore, localization of molecular techniques, especially Nasted-PCR in the country is recommended to diagnose Q fever. Also, the goat milk and goat population in Lorestan province should be considered as an important factor in the epidemiology of Q fever and consequently general health.