What is the workup for autoimmune problems?

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Last updated: October 17, 2025View editorial policy

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Diagnostic Work-up for Autoimmune Diseases

The comprehensive diagnostic work-up for autoimmune diseases should include inflammatory markers, complete blood count, autoantibody panels, and organ-specific tests based on clinical presentation to accurately diagnose and monitor autoimmune conditions. 1

Initial Laboratory Evaluation

  • Complete blood count (CBC) with differential is necessary to assess for cytopenias which are common in many autoimmune conditions 1, 2
  • Inflammatory markers including erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) should be evaluated to assess disease activity 1, 2
  • Comprehensive metabolic panel including liver and kidney function tests should be performed to assess for organ involvement 1, 2
  • Antinuclear antibody (ANA) testing should be used as a screening tool for many systemic autoimmune diseases 1
  • Rheumatoid factor (RF) and anti-cyclic citrullinated peptide (anti-CCP) antibodies should be tested for suspected inflammatory arthritis 1, 2

Disease-Specific Testing

  • For suspected systemic lupus erythematosus, anti-dsDNA, anti-Smith, anti-RNP, anti-SSA, anti-SSB antibodies should be tested 2
  • For suspected systemic sclerosis, anti-centromere, anti-Scl-70, anti-RNA polymerase III antibodies should be tested 2
  • For suspected autoimmune hepatitis, anti-smooth muscle antibodies, anti-liver kidney microsomal antibodies, and serum immunoglobulins should be tested 3, 2
  • For suspected myositis, creatine kinase (CK), transaminases (AST, ALT), lactate dehydrogenase (LDH), aldolase, and myositis-specific antibodies should be tested 3, 2
  • For suspected autoimmune thyroid disease, thyroid function tests (TSH, free T4) and thyroid antibodies (anti-TPO, anti-thyroglobulin) should be tested 2

Organ-Specific Testing

  • For inflammatory myopathies: CK, transaminases, LDH, aldolase, and troponin (to evaluate cardiac involvement) 3, 2
  • For autoimmune hepatitis: liver function tests, serum immunoglobulins, and liver-specific autoantibodies 3, 2
  • For chronic spontaneous urticaria: differential blood count, C-reactive protein/ESR, IgG-anti-TPO, and total IgE levels 3
  • For pulmonary alveolar proteinosis: GM-CSF antibody testing is recommended for all patients with suspected or confirmed PAP syndrome 3

Imaging Studies

  • Joint radiographs should be performed for suspected inflammatory arthritis 1
  • Abdominal ultrasound or CT scan should be performed to evaluate for organomegaly in suspected systemic disease 1
  • Muscle MRI should be performed for suspected inflammatory myopathies 3, 1
  • For pulmonary involvement, chest imaging (X-ray or CT) should be performed 3

Additional Diagnostic Procedures

  • For suspected autoimmune hepatitis, liver biopsy is considered essential for definitive diagnosis 3, 1
  • For suspected pulmonary alveolar proteinosis, bronchoalveolar lavage (BAL) should be performed as part of the diagnostic work-up 3
  • For suspected myositis with uncertain diagnosis, electromyography (EMG), MRI, and/or muscle biopsy should be considered 3

Pre-Treatment Testing

  • Testing for latent tuberculosis, hepatitis B, and hepatitis C should be performed before starting immunosuppressive therapy, especially rituximab 3, 4
  • Complement levels (C3, C4, CH50) should be tested for suspected lupus or complement deficiencies 2
  • HLA typing (particularly HLA-B27) should be performed for suspected spondyloarthropathies 2

Common Pitfalls to Avoid

  • Relying solely on autoantibody testing without clinical correlation can lead to misdiagnosis 1, 2
  • Delaying treatment while awaiting complete diagnostic work-up in severe presentations can worsen outcomes 3, 1
  • Not screening for infectious diseases (HIV, hepatitis, tuberculosis) before starting immunosuppressive therapy can lead to serious complications 3, 4
  • Failing to monitor immunoglobulin levels in patients receiving rituximab, as hypogammaglobulinemia is a common side effect 4

Monitoring Disease Activity

  • Regular monitoring of inflammatory markers (ESR, CRP) should be performed to assess treatment response 1, 2
  • Disease-specific autoantibodies should be monitored to assess disease activity when appropriate 1
  • Organ function tests should be monitored based on systems involved 1, 2
  • For patients on rituximab therapy, immunoglobulin levels should be monitored due to risk of hypogammaglobulinemia 4

References

Guideline

Diagnostic Work-up for Autoimmune Diseases

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

Guideline

Autoimmune Disease Diagnosis and Monitoring

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

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