It is astounding to consider that virtually, every textbook of physiology in every medical school in the world does not include a chapter on immunology. On the other hand, virtually, in every textbook in internal medicine, immunology and immune response overlaps with every tissue and every organ. Indeed, historically, the concept of the immune response was recognized primarily in the setting of allergy and/or anaphylaxis. Indeed, the very concepts of infection, microbiology and host protection are relatively new sciences. In fact, it was little more than 100 years ago when washing hands became what is now coined “standard of care.” How different it is in 2013, where one finds Handi Wipes for shoppers to use at grocery stores to protect themselves from the flora on shopping cart handles. Autoimmunity is even a newer concept without going into the well-known history of Paul Ehrlich and hemolytic anemias, the LE cell, and the beginning field of serology (and rheumatoid factor discovery). It is apparent that our understanding of autoimmunity has become linked hand-in-glove with new tools and investigational probes into serology and, more recently, the cellular immune response. With such discoveries, a number of key observations stand out. Firstly, there are a great deal more autoantibodies than there are autoimmune diseases. Second, there are a great deal more of autoimmune diseases than was believed in 1963 on the occasion of the publication of the first textbook of autoimmune diseases. Third, autoimmune diseases are, for the most part, orphan diseases, with many entities afflicting too few patients to excite the financial limb of pharmaceutical companies. In this special issue, we have grouped a number of papers, many of which were presented at the recent Congress of Autoimmunity that focus on issues that are not commonly discussed in autoimmunity. It reminds us that due to the ubiquitous nature of the innate and adaptive response, that there are a large number of diseases that have either an inflammatory and/or specific autoimmune response, we have to keep an open eye because everything is potentially autoimmune until proven otherwise.