HE is a diagnosis of "exclusion."

Alternative diagnosis

must be ruled out (examples):

  • Toxic, infectious or metabolic causes.

  • Nutrient deficiencies (especially B vitamins- potentially masked by MTHFR gene variants)

  • Other autoimmune encephalitis with known antibodies (see here)

  • Traditional (non-autoimmune) epilepsy

  • Complications of thyroid disease

  • Migraine variants

  • Parathyroid tumors

  • Adrenal insufficiency



Testing blood and spinal fluid for:

  • Antithyroid autoantibodies including Thyroid Peroxidase Antibody (TPO) or Thyroglobulin Antibody (TgAb)


  • Thyroid and Stimulating Hormone Receptor Antibody (TRAb)


  • Check for the presence of other antibodies associated with cognitive or psychiatric symptoms such as Anti-NMDA Receptor (NMDAR) encephalitis or other AE's. (See here)


  • Vital lab tests to rule out life-threatening or debilitating conditions such as viral or bacterial encephalitis, meningitis or Creutzfedt-Jakov disease. 


  • Check for presence of inflammation markers such as C-reactive protein or erythrocyte sedimentation rate (ESR)


  • Protein levels


  • Glucose levels


  • Oligoclonal bands


  • Opening pressure in the CSF


  • Checked for significant vitamin deficiency


  • Presence of heavy metals

PET or SPECT scans to look for hypoperfusion or hypometabolism

MRI to check for evidence of physical damage to brain

EEG to look for evidence of seizure-activity or of noticeable slight slowing

Neuropsychological testing to objectively identify specific areas and degrees of impairment.


Tips for Dealing with side effects of IVIG, Steroids and PLEX

**Please remember these are just suggestions, check with your doctor first and let them know about any discomfort you may have**


The most important thing to know about treatments is that for an autoimmune encephalitis like Hashimoto's Encephalopathy is that your main treatment will be one or more of something called an immune suppressant.

Because your bodies are all different and the AE is not always the same- there is not one set type of treatment for all of us. This includes any other medications - we don't all take or respond the same way to them.

It is also important to note that for many (not all) who have an AE, antipsychotics can actually make them feel worse and can potentially cause harm to the brain. It is important to speak to your doctor about this if they prescribe it to you.

Immune Suppresive Treatments

First line of treatment for HE, typically (and other AE's)

Note: Patients may not receive treatments in this order and may also be prescribed combinations of treatments.


Corticosteroids: Usually the first line of treatment is corticosteroids. That is becasue 90% of patients with HE respond to it and it is both inexpensive and readily available.​ For severely affected patients who have been hospitalized, treatment is often initiated with a high dose course of intravenous corticosteroids such as 1g/day for 3-7 days. Symptoms in some patients may begin to alleviate within as little as 1-2 days after initiating treatment, although improvement is more commonly seen on or after day 3 or 4. After, patients often return home with an oral taper of prednisone for 6-12 months.

IVIG: (Intravenous Immunoglobulin) Applied intravenously through a vein or port. A solution of concentrated healthy antibodies from many blood donors. It boosts the body's immune response.

Plasmapheresis: (PLEX) An apheresis machine cleans the body's plasma containing the bad antibodies from the blood and replaces it with albumin or donor plasma. Administered by vein or ports.

Second line of treatment for HE (and other AE's)

Note: You may be prescribed others not listed here

Rituximab: (Rituxan) A biologic monoclonal antibody treatment that attacks B cells. It is administered intravenously through a vein or port. 

Cyclophosphamide: (Cytoxan) A strong type of chemotherapy that attacks the DNA in cells. Can be taken orally or by inection.

Cellcept: (Mycophenolate Mofetil) An immune suppressant taken orally. 

Tocilizumab: (Atlizumab) A biologic immune suppressant designed to inhibit parts of the immune system that cause inflammation by inhibiting the chemical signal interleukin-6 (IL-6). Administered by infusion into a vein, port or subcutaneous injection.

Methotrexate: Low dose chemotherapy drug in pill form.

Imuran: (Azathioprine) An immune suppressant taken orally

Plaquenil: (Hydroxychloroquine) It belongs to a class of medications known as disease-modifying antirheumatic drugs (DMARDs). It can reduce swelling/pain in arthritis and other autoimmune conditions.


Tips To Deal With Side Effects From Steroids, IVIG and Plasmapheresis

**Please remember that these are just suggetions. Check with your doctor about

any symptoms or discomfortsyou may have**


Make sure you are tapered off slowly: to avoid adenal insufficiency, which can be a very serious condition.

Use medication: like Zofran for nausea. For acid reflux depending how bad it is: tums or prilosec. Ginger or peppermint candy even help sometimes.

Anti- anxiety medication are sometimes prescribed: for those who respond to steroids with anxiety


Do not take ibuprofin (Motrin/Advil) beforehand: This can cause bleeding


Infusions can take several hours: bring something to eat, drink or a book or movie on your smart device.

Take Benedryl: before your infusion starts (often this may only happen for the first few times recieving IVIG)

Take Tylenol or Exdedrin: before and after infusion

Drink plenty of fluids: before and after

If you start to get a headache: ask them to slow down the drip rate

If you are getting sick: ask your doctor to change the IVIG drug


If during infusions you feel symtomatic tell your doctor or nurse right away. According to IG Living their chart below can help explain. IG Living Magazine which is free online.  



Do not take ibuprofin (Motrin/Advil) beforehand: This can cause bleeding


Drink plenty of fluids beforehand

Empty your bladder right before


If you are experiencing nausea: ask for a tums or calcium drip


If you are cold: ask for a heating blanket or blankets

Your mobility will be limited: Read, listen to music or rest during procedure

Notify your plasmapheresis technician immediately: if you should experience any of the following signs or symptoms: tingling of the lips, dizziness, lightheadedness, sweating, coldness, cramps, bleeding from a vein or from the catheter site, itching, wheezing, or a rash.


If you have a catheter or port: notify your doctor if you experience redness, heat, or swelling at the catheter site or if you have fever or chills.

Antipsychotics and side effects

"Note that because of the completely different disease mechanism, use of antipsychotic drugs commonly used to treat bipolar disorder and schizophrenia such as Clozapine (Clozaril) and Risperidone (Risperidal) may not be effective, and according to some clinicians may actually increase the severity of AE symptoms. This varies depending on the type of AE and where patients are in the treatment course. Prior to initiating immunotherapy, these medications are less likely to be helpful and more side effects may be seen.

Once the inflammatory process is being treated, these medications may be essential to reduce suffering from the symptoms of AE and maximizing functioning as patients recover.

Failure to respond to antipsychotics may be a diagnostic clue that the actual cause of psychosis may be autoimmune encephalitis. However, given not all patients with psychiatric disease respond to the first anti-psychotic tried, it is important to have psychiatrists involved in these cases to help guide diagnostic and treatment considerations, as well as looking for other symptoms which would also suggest AE (cognitive decline, seizures, abnormal movements, sleep disruption etc.)."

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This website is not a substitute for professional advice, and the content here is not intended for use in diagnosing, curing, or preventing disease. The site does not employ and is not overseen by medical professionals. Articles and studies listed here are intended solely for personal use and reference.  Although you will find a great deal of information about HE/SREAT on this website, HESA cannot provide medical advice. If you have HE/SREAT, or think you may have it, consult a qualified neurologist,

preferably one with experience addressing immune-mediated illness. 

© 2019 Hashimoto's Encephalopathy SREAT Alliance,  an Illinois not-for-profit corporation