• Acute Disseminated Encephalomyelitis (ADEM)
• Acute necrotizing hemorrhagic leukoencephalitis
• Addison's disease
• Agammaglobulinemia
• Alopecia areata
• Amyloidosis
• Ankylosing spondylitis
• Anti-GBM/Anti-TBM nephritis
• Antiphospholipid syndrome (APS)
• Autoimmune angioedema
• Autoimmune aplastic anemia
• Autoimmune dysautonomia
• Autoimmune hepatitis
• Autoimmune hyperlipidemia
• Autoimmune immunodeficiency
• Autoimmune inner ear disease (AIED)
• Autoimmune myocarditis
• Autoimmune pancreatitis
• Autoimmune retinopathy
• Autoimmune thrombocytopenic purpura (ATP)
• Autoimmune thyroid disease
• Autoimmune urticaria
• Axonal & neuronal neuropathies
• Balo disease
• Behcet’s disease
• Bullous pemphigoid
• Cardiomyopathy
• Castleman disease
• Celiac disease
• Chagas disease
• Chronic fatigue syndrome**
• Chronic inflammatory demyelinating polyneuropathy (CIDP)
• Chronic recurrent multifocal ostomyelitis (CRMO) 
• Churg-Strauss syndrome
• Cicatricial pemphigoid/benign mucosal pemphigoid
• Crohn’s disease
• Cogans syndrome
• Cold agglutinin disease
• Congenital heart block
• Coxsackie myocarditis
• CREST disease
• Essential mixed cryoglobulinemia
• Demyelinating neuropathies
• Dermatitis herpetiformis 
• Dermatomyositis
• Devic's disease (neuromyelitis optica)
• Discoid lupus
• Dressler’s syndrome
• Endometriosis
• Eosinophilic esophagitis
• Eosinophilic fasciitis
• Erythema nodosum
• Experimental allergic encephalomyelitis
• Evans syndrome
• Fibromyalgia**
• Fibrosing alveolitis
• Giant cell arteritis (temporal arteritis)
• Giant cell myocarditis
• Glomerulonephritis
• Goodpasture’s syndrome
• Granulomatosis with Polyangiitis (GPA) (formerly called Wegener's Granulomatosis)
• Graves' disease
• Guillain-Barre syndrome
• Hashimoto's encephalitis
• Hashimoto’s thyroiditis
• Hemolytic anemia
• Henoch-Schonlein purpura
• Herpes gestationis
• Hypogammaglobulinemia
• Idiopathic thrombocytopenic purpura (ITP)
• IgA nephropathy
• IgG4-related sclerosing disease
• Immunoregulatory lipoproteins
• Inclusion body myositis
• Insulin-dependent diabetes (type1)
• Interstitial cystitis
• Juvenile arthritis
• Juvenile diabetes
• Kawasaki syndrome
• Lambert-Eaton syndrome
• Leukocytoclastic vasculitis
• Lichen planus
• Lichen sclerosus
• Ligneous conjunctivitis
• Linear IgA disease (LAD)
• Lupus (SLE)
• Lyme disease, chronic 
• Meniere’s disease
• Microscopic polyangiitis
• Mixed connective tissue disease (MCTD)
• Mooren’s ulcer
• Mucha-Habermann disease
• Multiple sclerosis
• Myasthenia gravis
• Myositis
• Narcolepsy
• Neuromyelitis optica (Devic's)
• Neutropenia
• Ocular cicatricial pemphigoid
• Optic neuritis
• Palindromic rheumatism
• PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcus)
• Paraneoplastic cerebellar degeneration
• Paroxysmal nocturnal hemoglobinuria (PNH)
• Parry Romberg syndrome
• Parsonnage-Turner syndrome
• Pars planitis (peripheral uveitis)
• Pemphigus
• Peripheral neuropathy
• Perivenous encephalomyelitis
• Pernicious anemia
• POEMS syndrome
• Polyarteritis nodosa
• Type I, II, & III autoimmune polyglandular syndromes
• Polymyalgia rheumatica
• Polymyositis
• Postmyocardial infarction syndrome
• Postpericardiotomy syndrome
• Progesterone dermatitis
• Primary biliary cirrhosis
• Primary sclerosing cholangitis 
• Psoriasis
• Psoriatic arthritis
• Idiopathic pulmonary fibrosis
• Pyoderma gangrenosum
• Pure red cell aplasia
• Raynauds phenomenon
• Reactive Arthritis
• Reflex sympathetic dystrophy
• Reiter’s syndrome
• Relapsing polychondritis
• Restless legs syndrome
• Retroperitoneal fibrosis
• Rheumatic fever
• Rheumatoid arthritis
• Sarcoidosis
• Schmidt syndrome
• Scleritis
• Scleroderma
• Sjogren's syndrome
• Sperm & testicular autoimmunity
• Stiff person syndrome
• Subacute bacterial endocarditis (SBE)
• Susac's syndrome
• Sympathetic ophthalmia
• Takayasu’s arteritis
• Temporal arteritis/Giant cell arteritis
• Thrombocytopenic purpura (TTP)
• Tolosa-Hunt syndrome
• Transverse myelitis
• Ulcerative colitis
• Undifferentiated connective tissue disease (UCTD)
• Uveitis
• Vasculitis
• Vesiculobullous dermatosis
• Vitiligo
• Wegener’s granulomatosis (now termed Granulomatosis with Polyangiitis (GPA)

**NOTE Fibromyalgia and Chronic Fatigue are listed, not because they are autoimmune, but because many persons who suffer from them have associated autoimmune disease(s)