Endocarditis and vascular infections are common manifestations of persistent localized infection due to , and recently, fluorescence hybridization (FISH) was proposed as an alternative tool for their diagnosis. In this study, we evaluated the efficiency of FISH in a series of valve and vascular samples infected by We tested 23-positive valves and thrombus samples obtained from patients with Q fever endocarditis. Seven aneurysms and thrombus specimens were retrieved from patients with Q fever vascular infections. Samples were analyzed by culture, immunochemistry, and FISH with oligonucleotide and PNA probes targeting -specific 16S rRNA sequences. The immunohistochemical analysis was positive for five (17%) samples with significantly more copies of DNA than the negative ones ( = 0.02). FISH was positive for 13 (43%) samples and presented 43% and 40% sensitivity compared to that for quantitative PCR (qPCR) and culture, respectively. PNA FISH detected in 18 (60%) samples and presented 60% and 55% sensitivity compared to that for qPCR and culture, respectively. Immunohistochemistry had 38% and 28% sensitivity compared to that for FISH and PNA FISH, respectively. Samples found positive by both immunohistochemistry and PNA FISH contained significantly more copies of DNA than the negative ones ( = 0.03). Finally, PNA FISH was more sensitive than FISH (60% versus 43%, respectively) for the detection of We provide evidence that PNA FISH and FISH are important assays for the diagnosis of endocarditis and vascular infections.