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This presentation will review the current evidence-based approaches in the evaluation of autoimmune disease. Identification of the GI microbiota, food triggers, predictive auto-antibodies, and other predictive strategies, in the risk assessment, diagnosis and management of autoimmune diseases will be examined from an evidence-based perspective. These systemic disorders range from autoimmune inflammatory disorders, including rheumatoid arthritis, ankylosing spondylitis, to immunogenic thyroiditis (i.e., Graves and Hashimoto's disease), and degenerative neurological conditions such as multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS) and dementia. Within this framework the role of molecular mimicry in the genesis of autoimmune diseases will be fully explored. Novel diagnostic modalities and functional/metabolic objective laboratory assays, including emerging predictive antibody testing, in these applications will also be presented and critiqued. Finally, specific rational and efficacious integrative treatment interventions for these specific clinical situations will be offered.