Q fever infection can lead to chronic Q fever, a potentially lethal disease occurring in 1–5% of patients infected with Coxiella burnetii, characterized by the persistence of this intracellular bacterium. It usually presents as endocarditis, infected vascular aneurysms, or infected vascular prostheses. This systematic review of the literature discusses the various autoimmune syndromes and B-cell dyscrasias in acute and chronic Q fever patients, that may interfere with or impede recognition and diagnosis of Q fever.