10 Rare Autoimmune Diseases You’ve Probably Never Heard Of
Sep 03, 2025 By Isabella Moss

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Autoimmune diseases occur when the immune system mistakenly attacks healthy cells in the body. While conditions like lupus and rheumatoid arthritis are well-known, many rare autoimmune diseases remain unfamiliar to most. These little-known conditions can have serious impacts, highlighting the importance of raising awareness and improving understanding of their complexities.

1. Stiff Person Syndrome (SPS)

Stiff Person Syndrome belongs to a category of medical conditions that is not very common in medical conditions of the neurological disorder and expresses hardness in muscles and painful spasm. The immune system destroys some nerves used in transmitting nerve stimuli causing impairment of normal muscle activity.

Key Symptoms:

  • Muscle stiffness to extreme.
  • Seizures that cause paralyzing spasms when one suddenly moves or gets stressed out
  • Sensory loss that makes walking or standing hard

Often misdiagnosed as anxiety or multiple sclerosis, early detection can help manage symptoms with muscle relaxants and immune therapies.

2. Behçet’s Disease

Behçet’s Disease is a chronic condition that causes inflammation in blood vessels throughout the body. It can affect multiple systems, making it difficult to diagnose.

Key Symptoms:

  • Rather painful mouth and body sores
  • Joint pain
  • Eye inflammation
  • The problems of the digestive tract

If untreated, Behçet’s Disease can lead to serious complications, including vision problems and vascular damage.

3. Relapsing Polychondritis

Relapsing Polychondritis is a rare disorder marked by recurring inflammation of cartilage in the body, particularly in the ears, nose, and airways.

Key Symptoms:

  • Red, painful, or misshapen ears
  • Hoarseness or breathing issues
  • Joint pain and fatigue

The disease can affect major organs like the heart and lungs. Early recognition is crucial to preserving function and quality of life.

4. Dermatomyositis

This autoimmune condition affects the muscles and skin. It causes muscle weakness and distinctive rashes that usually appear on the face, chest, and knuckles.

Key Symptoms:

  • Purple or red rashes
  • Muscle pain and weakness
  • Difficulty swallowing

Dermatomyositis may be linked to underlying health conditions. Treatment often includes immunosuppressive medications and physical therapy.

5. Autoimmune Autonomic Ganglionopathy (AAG)

AAG is a rare autoimmune disorder that targets the autonomic nervous system, which controls involuntary bodily functions like heartbeat, blood pressure, and digestion.

Key Symptoms:

  • Dizziness or fainting when standing
  • Dry eyes and mouth
  • Abnormal sweating
  • Gastrointestinal issues

It can cause severe disruption to daily life. Accurate diagnosis through specialized antibody testing allows for targeted immune-based treatments.

6. Polymyositis

Polymyositis is a rare inflammatory myopathy characterized by chronic inflammation and progressive degeneration of skeletal muscles, particularly those located near the torso — such as the shoulders, upper arms, thighs, and hips. It primarily affects adults and tends to develop gradually, often leading to significant physical limitations over time.

Key Symptoms:

  • Persistent muscle weakness, especially in the proximal muscles (hips, thighs, shoulders, neck)
  • Difficulty with everyday tasks like climbing stairs, lifting objects, or rising from a seated position
  • Shortness of breath due to the potential involvement of chest muscles or the diaphragm
  • General fatigue, joint tenderness, and occasional low-grade fever

Polymyositis is often misdiagnosed as muscular dystrophy or age-related muscle loss due to symptom overlap. If left untreated, the condition can lead to irreversible muscle damage and disability. Prompt evaluation using muscle biopsies, enzyme tests, and imaging can support accurate diagnosis. Treatment often includes corticosteroids and immunosuppressive therapy to slow disease progression and restore function.

7. Vogt-Koyanagi-Harada Disease

Vogt-Koyanagi-Harada (VKH) disease is a multisystem autoimmune disorder that targets melanocyte-rich tissues — cells responsible for pigment production. The immune system erroneously attacks these cells in various organs, particularly in the eyes, inner ears, skin, and central nervous system, leading to widespread inflammation.

Key Symptoms:

  • Ocular symptoms: blurry vision, light sensitivity, pain, and inflammation (often bilateral uveitis)
  • Auditory issues: tinnitus, hearing loss, or imbalance due to inner ear involvement
  • Skin changes: depigmented patches (vitiligo-like), premature graying of hair, and scalp tenderness
  • Neurological signs: headaches, stiff neck, or even meningitis-like symptoms in early stages

VKH disease is a medical emergency in its acute phase. Without timely treatment, it may lead to permanent vision loss and hearing impairment. Due to its complex presentation, it is often mistaken for isolated eye conditions. High-dose corticosteroids and long-term immunomodulators are typically prescribed to control inflammation and preserve organ function.

8. Mixed Connective Tissue Disease (MCTD)

MCTD is a complex autoimmune condition that shares features of several diseases, including lupus, scleroderma, and inflammatory muscle diseases.

Key Symptoms:

  • Raynaud’s phenomenon (discoloration of fingers in cold)
  • Joint pain and swelling
  • Difficulty swallowing
  • Facial skin tightening

Because it mimics multiple conditions, it’s often overlooked. Timely medical intervention can prevent serious organ involvement.

9. Pemphigus Vulgaris

Pemphigus Vulgaris is a chronic autoimmune blistering disorder that targets desmogleins — proteins essential for cell-to-cell adhesion in the skin and mucous membranes. When the immune system attacks these proteins, the outer layers of the skin separate, forming painful blisters and erosions.

Key Symptoms:

  • Painful, fragile blisters in the mouth, throat, nose, or on the skin that rupture easily
  • Delayed healing of sores and development of crusted lesions
  • Widespread skin erosion and susceptibility to secondary infections
  • Weight loss or difficulty eating due to oral involvement

Without treatment, Pemphigus Vulgaris can be life-threatening due to fluid loss, malnutrition, and infections. However, it is manageable with prompt diagnosis and aggressive therapy. Treatment typically includes corticosteroids, immune-modulating medications, and meticulous wound care. Long-term monitoring is necessary, as relapses are common, especially when therapy is tapered too quickly.

10. Neuromyelitis Optica Spectrum Disorder (NMOSD)

Neuromyelitis Optica Spectrum Disorder is a serious autoimmune condition that predominantly affects the optic nerves and spinal cord. It results in demyelination — the stripping away of protective coverings around nerve fibers — leading to severe neurological deficits. NMOSD is distinct from multiple sclerosis but may initially appear similar in presentation.

Key Symptoms:

  • Rapid onset of vision loss in one or both eyes, sometimes accompanied by eye pain
  • Numbness, weakness, or paralysis in the legs or arms
  • Sudden bladder or bowel dysfunction due to spinal cord involvement
  • Severe episodes of nausea, vomiting, or hiccups if the brainstem is affected

NMOSD can lead to irreversible neurological damage if not recognized and treated early. It is commonly associated with antibodies targeting aquaporin-4, a protein found in central nervous system tissues. Distinguishing NMOSD from similar neurological conditions is essential, as standard treatments for other disorders may worsen symptoms.

Conclusion:

While these autoimmune conditions are considered rare, their impact on patients is anything but insignificant. Due to overlapping symptoms with more common illnesses, diagnosis is often delayed, leading to prolonged suffering and potential complications. Awareness is the first step in improving outcomes — both for individuals experiencing mysterious symptoms and for healthcare providers evaluating complex cases.

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