The complement system is a crucial part of our immune defense as, upon recognition, it can kill pathogens fast and effectively. However, misguided complement activation could cause damage to host tissues. Therefore, a well-controlled regulation of the complement system is a necessity to prevent collateral damage. Regulation is achieved by several complement inhibitory proteins, acting at different levels of the complement system. One of these complement regulators is factor H, the main regulator of the alternative complement activation pathway. Factor H can regulate the complement system both in fluid-phase and on the host cell surface by, for example, acting as co-factor for factor I, inactivating C3b. The functional properties of factor H are located within different regions of the protein. Functional impairment of factor H, either because of genetic variants, competing proteins such as the factor H-related proteins and proteins from certain pathogens, but also the presence of autoantibodies will impact on complement activation. However, exact consequences are dependent on the region within factor H that is affected. Autoantibodies binding to factor H have been shown to inhibit several regulatory functions of factor H, which is observed in diseases such as membranoproliferative glomerulonephritis and atypical hemolytic uremic syndrome. As more recently the presence of anti-factor H autoantibodies has also been discovered in several other diseases, ranging from autoimmune diseases to cancer, this review provides an overview of the presence of factor H autoantibodies described in these diseases. Factor H autoantibodies are reported to have inhibitory, or enhancing, effects on factor H, depending on the epitopes that are recognized. Formal conclusions about the pathogenicity of the factor H autoantibodies in some of these diseases cannot be drawn yet. Importantly, understanding the binding and functional impact of anti-factor H (auto)antibodies will allow targeted interventions to diminish pathological consequences of anti-factor H autoantibodies but may also open up additional avenues for the use of anti-factor H antibodies as therapeutic agents.