Q fever is a zoonotic disease of public health significance caused by Coxiella burnetii affecting animals' productive and reproductive capabilities. This study aimed to compare seroprevalence of anti C. burnetii IgG and IgM antibodies (Abs) in cows and buffaloes in Egypt. Total of 314 serum and 282 milk samples were collected from 546 cows, and 50 buffaloes located in Assuit, Bani-Swif, Dakahlya, Fayoum, Giza, and Minya Governorates from 2015 to 2017. Animal reproductive status was recorded. Anti-Coxiella Abs were detected using Immuno-Fluorescent Antibody assay (IFA). In addition, seropositive samples were subjected to qPCR targeting isocitrate dehydrogenase-deficient (icd) gene. Differences in seropositive IgG and IgM in serum and milk samples among animal species, Governorates and animal reproductive status were investigated. In this study, overall seroprevalence of C. burnetii Abs was 31.5% (188/596). Considering sample type, IgG positive exceeds that of IgM in both sera and milk. IgG seroprevalence was significantly higher in serum (25.5%) than in milk (14.2%). In addition, within serum, IgG was significantly higher than IgM (12.1%). No significance was found between Governorates in IgG or IgM neither in serum nor in milk. However, significant higher seropositive IgG over IgM was observed in Assuit, Beni-Swif and Minya with 21.7, 24.5 and 23.9%, respectively. Regarding animal species, seroprevalence in cows (20.9%) was higher than in buffaloes (12.0%). IgG seroprevalence of cows was significantly higher in serum (26.0%) than milk (14.8%). In addition, within serum, seropositive IgG was significantly higher than IgM (12.5%). Both IgG and IgM seropositive were significantly the highest in abortion. Also, IgG seropositive was significantly higher in repeat breeder than apparent healthy. In buffaloes, only IgM seropositive was significantly the highest in abortion. In cows' sera, significant higher IgG over IgM was observed in all reproductive status. While in cows' milk samples, only abortion showed significant higher IgG over IgM. In buffaloes, no significant difference was observed between IgG and IgM neither in sera nor in milk. The icd gene of C. burnetii was detected only in 6 milk (8.6%) and 2 serum samples (1.7%). (In conclusion, the study revealed a wide distribution of infections over the study area. To set a preventive and control strategies of Q fever, further epidemiological studies are recommended. The study recommends using IgG in studying Q fever seroprevalence).