During 2008-2011, we tested 874 blood samples from febrile patients who had a fever >37.5°C, and 207 surface samples in households for Coxiella burnetii DNA in two rural Senegalese villages (Dielmo and Ndiop). Fisher's exact test and Spearman's correlation coefficient were used for statistical analysis. We identified four blood samples as positive for Coxiella burnetii DNA. The prevalence of Q fever in all tested samples was 0.46% in the two villages. C. burnetii DNA was also found in 7.5% of the dust samples in Ndiop, and in 0.9% in Dielmo; the prevalence in households was 22.6% in Ndiop and 2.6% in Dielmo. In Ndiop we found a weak correlation between positive environmental samples and the occurrence of the disease. Our findings show an association of environmental C. burnetii with human Q fever cases in a recently identified endemic area in rural Senegal.