Autoinflammatory Diseases are disorders of the Innate Immune System whereas Autoimmune Diseases are disorders of the Adaptive Immune System.

There are many overlapping symptoms such as fatigue, brain fog, malaise, fever, joint pain, swelling, rashes, neuropathy, gastrointestinal involvement, etc. between Autoimmune and Autoinflammatory Disease.

Overlapping symptoms between Autoinflammatory Disease and Autoimmune Disease can cause Autoinflammatory Diseases to be missed or misdiagnosed as Autoimmune Diseases. Diagnostic differentiation can be challenging as Autoinflammatory Diseases and Autoimmune Diseases involve immune system dysregulation and inflammation. Inflammation can be systemic (affecting multiple systems) or localized (organ-specific) in either and symptoms can range from mild to severe. Both Autoimmune Disease and Autoinflammatory Disease can be substantially debilitating. 

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One of the key differentiating pieces is that Autoinflammatory Diseases do not have the high antibody titers or the antigen-specific T-cells that are characteristic of Autoimmune Diseases.

Some researchers believe that Autoimmune and Autoinflammatory Diseases could be a part of a spectrum of inflammatory disorders rather than two distinct groups.