We are seeing more autoimmune disorders related conditions today than ever before in medicine. Two key contributing factors to this phenomena include changes in our food supply and alterations in gastrointestinal health. This is important because in order to effectively treat autoimmunity we have to know where it is coming from. We see many cases where patients arrive at our clinic and these factors have not been addressed. We also observe that when accounted for eating a low-inflammation and immune-neutral diet along with normalization of the gastrointestinal ecology many autoimmune disorders symptoms improve.