Anti-cytokine autoantibodies (AAbs) are frequent and involve a very large panel of cytokines both in healthy subjects and in patients with various pathological conditions. In healthy individuals, anti-cytokine AAbs are described as a part of the natural AAb repertoire and are thought to contribute to the fine regulation of cytokine homeostasis. In some patients, neutralizing AAbs targeting cytokines required for the immune protection against specific microbes may induce acquired immunodeficiency leading to very specific infectious phenotypes. For instance, anti-IFNγ AAbs may induce disseminated non-tuberculous mycobacterial infections; anti-IL-17 AAbs are associated with the development of chronic mucosal candidiasis, and anti-IL-6 AAbs with severe staphylococcal or streptococcal infections. In patients with autoimmune diseases, AAbs directed against pathogenic cytokines are able to influence the course of the diseases. In lupus patients, neutralizing anti-IFNα and anti-TNFα AAbs are associated with a decreased bioactivity of the corresponding cytokine and a lower disease severity. Similarly, anti-IL-1α AAbs are associated with nondestructive forms of chronic polyarthritis. More surprisingly, neutralizing anti-BAFF AAbs are observed in the serum of lupus patients with elevated IFNα signature and higher disease activity. In this review, we summarize the current literature describing the different phenotypes and the main mechanisms associated with the occurrence of anti-cytokine AAbs.