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. Reportedly, high concentrations of anti-cardiolipin antibodies may be found in acute Q fever patients, while specifically cardiac muscle antibodies have been reported during chronic Q fever. Systemic lupus erythematosus and antiphospholipid syndrome are the most frequently reported autoimmune syndromes, followed by neuromuscular disorders and vasculitis. B-cell dyscrasia, mostly cryoglobulinaemia, is predominantly described in chronic Q fever patients with endocarditis. We conclude that immunological (epi)phenomena are not rare during Q fever and may obscure the infectious etiology of the disease.