All Conditions & Treatments

How Lupus Affects Multiple Organs

Adapted from a talk to the SLE Workshop at Hospital for Special Surgery

Illustration of kidneys.

The many faces of lupus

It is difficult for many to fully understand the complexity of a disease like lupus. While there are typical cases and standard symptoms, lupus can affect different organs in the body in various ways, which makes the diagnosis that much more difficult. The patient cases featured in this article illustrate the many ways that lupus can impact different organs in the body and – in one case – appear to be present in a person who in fact did not have lupus.

Lupus overview

Systemic lupus erythematosus (SLE or commonly called "lupus") is an autoimmune disease that impacts the immune system. The immune system is like an organ in the body. It is made up of blood cells and lymph nodes as well as parts of the liver and the spleen. The immune system normally protects your body against invaders and infection using proteins called antibodies. However, in certain situations, the antibodies of the immune system recognize parts of a person’s own body as foreign, which results in conditions called autoimmune diseases.

Lupus is a chronic condition in which people experience periods of activity and remission. It is characterized by inflammation that starts on a molecular and cellular level and, eventually, enters a level at which symptoms become visible. There is no cure for lupus, and it is diagnosed based on a combination of symptoms, physical exam findings, and blood test results. Other facts about lupus:

  • No two cases are alike.
  • 90% of those diagnosed with lupus are female.
  • 15% of those diagnosed with lupus are children or adolescents.

Lupus is a complex and challenging disease that can involve any organ system in the body. Some of the organ systems that can be affected by lupus or lupus medications are:

Diagnosing lupus

One of the most challenging aspects of lupus is making the diagnosis, since the disease can impact any of the body’s organs and cause patients or doctors to be distracted or focused on a particular organ. Diagnosis of lupus involves putting together a variety of different pieces of information.

The American College of Rheumatology (ACR) have issued a list of criteria for classification sometimes used for making a diagnosis, but also used to evaluate whether a patient is qualified to participate in a research study on lupus. This list includes:

  • positive antinuclear antibody (ANA)
  • fever
  • blood disorder – certain types of anemia (low red blood cell count), leukopenia (low white blood cell count), or thrombocytopenia (low platelet count)
  • neurological disorder – delirium, psychosis, or seizures
  • mucocutaneous – certain types of alopecia (hair loss), mouth sores, or rashes, including malar rash (a rash over the cheeks and nose, often in the shape of a butterfly) or discoid rash (a rash that appears as red, raised, and disk-shaped patches)
  • serositis – inflammation of the lining around the lungs (pleuritis) or inflammation of the lining around the heart that causes chest pain that is worse with deep breathing (pericarditis)
  • musculoskeletal – joint pain and swelling
  • kidney disorder – persistent protein or evidence of lupus involvement on kidney biopsy
  • immunologic disorder – anti-dsDNA or anti-Smith or antiphospholipid antibodies or low complement levels

Clinical case studies

These patients were chosen due to their complexity, which provides an opportunity to demonstrate and explore the impact of lupus on different organ systems. These cases do not necessarily represent the typical lupus patient. The names of patients and any identifying features have been changed.

Case example: "Alicia" – kidneys and skin

Alicia is a 27-year-old woman who was admitted to the hospital with a variety of symptoms, including:

  • fatigue and malaise for over two months
  • malar rash that became worse with sun exposure
  • arthritis (pain and swelling) in her hands and knees
  • high blood pressure
  • newly discovered kidney dysfunction

After a full examination that involved a discussion of symptoms and blood and imaging tests, Alicia was diagnosed with multi-organ-involvement lupus with lupus nephritis. This case illustrates how lupus can affect the kidneys and the skin.

How lupus can affect the kidneys

One of the jobs of the kidneys is to clean the blood by filtering it and producing urine, which then drains into the bladder and is finally expelled. Lupus nephritis develops when inflammation affects portions of the kidneys, often causing difficulties with releasing urine and therefore producing swelling in areas of the body such as the face, hands, legs, and feet due to fluid retention. This is often worse in the morning. Additionally, patients may experience high blood pressure, bloody urine (pink or brown), protein in the urine (foamy urine or bubbles in the toilet), fatigue, weight gain (due to excess fluid retention), or decreased urination.

There are multiple types of nephritis (inflammation of the kidneys). Doctors base their diagnosis of lupus nephritis on the patient’s symptoms, an evaluation of blood tests and urinalysis, and, often, a kidney biopsy. Blood testing includes measuring creatinine levels. If creatinine levels are high, this indicates that the kidneys are not functioning correctly. A urinalysis is conducted to look for protein and blood cells in the urine, as well as to measure the protein/creatinine ratio. A kidney biopsy is used to determine the type of nephritis a patient has.

Treatments for lupus nephritis often involve the use of steroids given by mouth and/or intravenously. Patients who are extremely ill are generally given cyclophosphamide (Cytoxan), mycophenolate mofetil (Cellcept), or mycophenolic acid (Myfortic). Other options include azathioprine (Imuran), belimumab (Benlysta), tacrolimus (Prograf), and rituximab (Rituxan). Blood pressure medications (such as lisinopril or enalapril) are often given to control blood pressure as well as help the kidneys keep proteins in the body and prevent them from spilling into the urine.

How lupus can affect the skin

Lupus can produce a variety of different rashes, and Amanda had the most common one: the malar rash or “butterfly” rash (so named for the shape it makes across the nose and cheeks). However, patients may experience rashes anywhere on the body such as lacey rashes on the arms or discoid rashes on the scalp, face and inside the ears − often leaving scars. There are other, less common rashes, such as bullous rashes that produce blisters, chilblains (red or purplish skin sores), and psoriasiform rashes. It is important to determine whether rashes are due to lupus or to other conditions, like a fungal or bacterial infection. Depending on the nature of the rash, the patient may be sent to a dermatologist for a skin biopsy.

Treatment for rashes includes topical creams, lotions, or ointments. Many patients take hydroxychloroquine (Plaquenil) for extended periods of time, which can be good for treating lupus of the skin and many other symptoms.

Case example: “Jason” – Nervous system and blood

Jason is a 19-year-old man who was admitted to the hospital with a variety of symptoms including:

  • confusion
  • weight loss
  • hand rash
  • low blood cell counts
  • abnormal liver tests
  • muscle inflammation and abnormal muscles tests

Jason was diagnosed with central nervous system (CNS) lupus, which involves the brain and spinal cord. Jason presented with cytopenias (low blood cell counts), hepatitis (inflammation of the liver), and myositis (inflammation of the muscle). Jason’s case demonstrates how lupus can impact the nervous system and the blood.

How lupus can affect the nervous system

Lupus that impacts the central nervous system, called “CNS lupus,” is less common than other forms of lupus and can create numerous symptoms and issues for patients because it reaches out beyond the brain and spinal cord to affect other parts of the body. CNS lupus can cause a number of issues, including confusion, brain fog (cognitive dysfunction), seizures, changes in personality, or stroke. Lupus that affects the peripheral nervous system may cause neuropathy (damage to the nerves), which could result in numbness and tingling. Lupus of the nervous system is often co-managed by a rheumatologist and a neurologist.

CNS lupus can be challenging to diagnose because there are many other things that can cause issues with the brain or the spinal cord. Due to the complexity of CNS lupus, a number of tests may be ordered to determine more specific information.

A CT scan and/or MRI may be used to examine the anatomy of the brain to check for abnormalities.

An EEG (electroencephalogram) may be used to evaluate for seizures.

A lumbar puncture (“spinal tap”) may be used to analyze for infection or inflammation in the spinal fluid that surrounds the brain and spinal cord.

An EMG/NCS (electromyelogram/nerve conduction study) may be used to evaluate for neuropathy.

The treatment for CNS lupus varies, depending on the symptoms experienced by the patient.

How lupus can affect the blood

To fully understand the impact of lupus on the blood, it is important to know the different types of blood cells and their roles:

  1. White blood cells produce antibodies, help fight infections, and promote healing.
  2. Red blood cells deliver oxygen throughout the body
  3. Platelets help blood to clot.

Lupus in the blood can lead to a number of issues that impact all three different types of blood cells. Each patient is different in the way that lupus affects their blood cells. Some may have low blood cell counts across the board, and others may have low blood cell counts of one or two specific types of blood cell.

Low white blood cell counts may increase the risk for infection. Low platelet counts may increase the risk of bleeding. When red blood cell counts are low it is called anemia. People with chronic disease who consistently experience inflammation throughout the body may be more at risk for a type of anemia called "anemia of chronic inflammation." There is also an increased risk of anemia in those with kidney disease. Another cause of anemia is hemolysis, where the red blood cell count decreases due to red blood cells coming apart. Symptoms of anemia may include fatigue, lightheadedness, and more.

Phlebotomy (blood draw) is used to determine whether lupus is impacting the blood. In rare instances, a patient may require a bone marrow biopsy.

In some cases, there may be no action taken in terms of treatment. Other treatments include steroids or other lupus medications such as Cellcept, Imuran, Rituximab, or intravenous immunoglobulin.

Case example: “Harmony” – Heart and bones

Harmony is a 36-year-old woman who has had lupus for 18 years. Harmony presented with a number of symptoms including:

  • alopecia (hair loss)
  • discoid rash
  • arthritis
  • lupus nephritis
  • cardiomyopathy
  • avascular necrosis of multiple joints

Harmony’s case demonstrates the ways in which lupus can impact the heart and the bones.

How lupus can affect the heart

It is important to understand the way the heart works in order to discuss how lupus may cause issues in the heart.
Deoxygenated blood enters the heart through the superior vena cava and is pumped into the right atrium, then through a valve called the tricuspid valve and into the right ventricle. From there the blood moves through the pulmonary valve into the pulmonary artery and is pumped into the lungs. In the lungs, the blood is filled with oxygen and deposited back into the heart through the pulmonary vein and into the left atrium. The now oxygenated blood moves from the left atrium through a valve called the mitral valve into the left ventricle. From the left ventricle the oxygenated blood is pumped out of the heart through the aortic valve into the aorta and on to the rest of the body.


The walls of the heart are made up of muscle. In some patients with lupus there can be inflammation and weakening of the heart muscle that can result in less effective pumping of the heart. This was the case with Harmony and is called cardiomyopathy.

People with lupus also can experience problems with the heart valves. The valves may not open and close properly. Sometimes clumps (sometimes called “vegetations”) will develop on the valves that may be from lupus or may be caused by an infection not directly related to lupus.


Another common impact of lupus is called pericarditis, which is irritation and inflammation of the sac lining the heart or pericardium. Patients with pericarditis may experience chest pain that may worsen when they lie on their back. Patients may also experience a pericardial effusion which is a build-up of fluid in the pericardium.

Tests and treatments for heart conditions caused by lupus

The tests used to look for cardiomyopathy, valve disease or pericarditis would be an EKG and echocardiogram (an ultrasound of the heart). Treatments for cardiomyopathy may include steroids or other lupus medications. Those with valve disease may need blood thinners or antibiotics for treatment.

Treatment for pericarditis and pericardial effusion may include anti-inflammatories, or in more severe pericardial effusion, they may need to be treated with steroids or have the fluid drained. Other lupus medications such as Imuran, Cellcept or Benlysta can also be used for treatment of these conditions.

How lupus can affect your bones

Harmony has avascular necrosis. This occurs when there is a lack of blood flow to certain parts of the bone that results in damage to that area of the bone. Avascular necrosis occurs more commonly in patients who take high doses of steroids for a prolonged period of time. An X-ray or MRI can be used to evaluate a patient for avascular necrosis. Treatment is rest and pain medication, and sometimes joint replacement surgery is needed. Medications to improve bone quality sometimes are considered.

Bone issues also may be caused by medications used to treat lupus. In particular, people who have taken steroids for long periods of time are at risk for issues with their bones. They may experience a thinning of the bone and decrease in bone density. Osteopenia is a mild thinning of the bone and decrease in bone mineral density. Osteopenia is a precursor to osteoporosis. Osteoporosis is a more significant thinning of the bone and decrease in bone mineral density.

The test for osteopenia and osteoporosis is a bone density test (DEXA scan). In the general population this test is usually given to women who have experienced menopause. Those taking steroids or with other risk factors for bone thinning may need to take this test at younger ages. The treatment for either osteopenia or osteoporosis may include calcium supplements, vitamin D, bisphosphonates (such as alendronate/Fosamax), parathyroid hormone (teriparatide/Forteo), denosumab (Prolia), and weight-bearing exercise. Learn more by reading Lupus, Osteoporosis and Bone Health.

Case study: “Josephine” – When "the great imitator" fools doctors

Josephine is a 55-year-old woman who was referred by her general practitioner because he thought she had lupus. She presented with:

  • diffuse body pain (changing location and intensity)
  • abdominal pain
  • difficulty walking
  • poor coordination
  • a positive ANA test

Josephine was examined and her neurological exam was abnormal. An MRI was administered that showed Josephine did not have lupus but instead had spinal stenosis of the cervical spine (narrowing of the cervical spine) with spinal cord compression. The symptoms were caused by spinal issues and Josephine just happened to have a positive ANA. Some people may have a positive ANA, and this is not a clear indicator that they have a lupus or any autoimmune diseases.

Lupus: The “great imitator”

The diagnosis of lupus is extremely complicated. As Josephine’s case demonstrates, some doctors may diagnose lupus when the cause is actually another condition. Similarly, the diagnosis of lupus can be challenging to make. In fact, lupus is often called “the great imitator” because it can mimic the symptoms of many other diseases. When doctors are looking for a diagnosis, they will have to consider any number of other diseases/conditions. For example, a doctor will have to look at the possibility of other rheumatic diseases, infections, heart disease, kidney disease, or even cancer before conclusively diagnosing lupus.

An important aspect of lupus is that no two patients’ stories are exactly the same. Even though there may be similarities, every person’s lupus experience is unique. The above case studies were complex examples of how lupus may present. A more common presentation is a combination of rashes, fatigue, or abnormal blood test results. Some patients may have only abnormal blood tests with no presenting symptoms. Lupus can run the gamut between more severe cases, like the ones presented here, to extremely mild cases. Many patients with lupus-like symptoms in fact have other conditions. People with sarcoidosis, for example, can present with a wide variety of symptoms and, like lupus, is known as an "imitator" or "mimicker" of other conditions. 

Once a patient is diagnosed with lupus, they may find that their doctors will want to blame their lupus for any health-related issues. Patients and doctors need to take into consideration that new symptoms may be caused by something besides lupus. Like anyone else, people with lupus can also experience common conditions, such as gallstones, bug bites, ovarian cysts, stomach or sinus infections.

Recommendations for patients

  • Include a primary care physician, in addition to a rheumatologist, as part of your team of doctors. Other medical specialists may become involved, depending on your symptoms.
  • Discuss new symptoms with all your doctors to get different perspectives.
  • Do not automatically assume that a new symptom is related to your lupus.

Lupus symptoms may change over time and impact any number of systems in the body. It is important for the physician to understand the patient’s life and goals when determining the right course of treatment and to prevent future issues.

This article is based on a 2015 presentation by Dr. Levine to the SLE Workshop at HSS, a free support and education group held monthly for people with lupus, their families and friends. It was reviewed and updated in 2023 by Dr. Lieber. Original article summary by Gwyneth Kirkbride, Social Work Intern, Department of Social Work Programs.


Alana B. Levine, MD
Assistant Attending Physician, Hospital for Special Surgery
Clinical Associate, Barbara Volcker Center for Women and Rheumatic Diseases

Sarah B. Lieber, MD, MS
Assistant Attending Physician, Hospital for Special Surgery
Assistant Professor of Medicine, Weill Cornell Medicine

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