6 Causes Of Autoimmunity Brain Fog (Plus Fixes)
If you’re living with an autoimmune disease like lupus, rheumatoid arthritis, or Hashimoto’s thyroiditis, you may have experienced the frustrating phenomenon known as brain fog—that cloudy, sluggish feeling that makes it hard to focus, remember things, or even string thoughts together. Alongside brain fog, many people with autoimmune conditions also deal with brain inflammation, which can worsen cognitive symptoms and impact daily life. But why do these issues occur, and what does science say about the connection between autoimmunity, brain fog, and inflammation? In this article, we’ll dive into the latest research to uncover the mechanisms behind these symptoms and share practical tips for managing them.
The Autoimmune-Brain Connection
Autoimmune diseases occur when the immune system mistakenly attacks healthy tissues, and this overactive immune response doesn’t always stay confined to joints, thyroids, or other peripheral tissues—it can affect the brain, too. Research shows that brain fog and brain inflammation in autoimmune conditions stem from several key mechanisms:
1. Neuroinflammation: The Immune System’s Ripple Effect
When the immune system is in overdrive, it releases pro-inflammatory cytokines (like IL-6 and TNF), which are signaling molecules that can cross into the brain and disrupt neural communication. This process, known as neuroinflammation, slows down brain activity, leading to symptoms like brain fog, fatigue, and difficulty concentrating.
A 2019 study found that even mild inflammation, triggered by a vaccine in healthy volunteers, reduced alertness and cognitive performance. For people with chronic autoimmune diseases, this inflammation is ongoing, constantly taxing the brain. Microglia, the brain’s immune cells, also play a role. When activated by systemic inflammation, they release cytokines that impair neuron function, contributing to cognitive sluggishness and even mood changes like depression.
2. Autoimmune Encephalitis: When Antibodies Attack the Brain
In some autoimmune conditions, such as autoimmune encephalitis or Hashimoto’s encephalitis, the immune system produces autoantibodies that directly target brain cells. These antibodies disrupt synaptic function, leading to memory loss, confusion, and brain fog. For example, a 2018 study highlighted how autoimmune encephalitis is increasingly recognized as a cause of cognitive impairment, with symptoms driven by antibodies attacking critical brain receptors.
Conditions like steroid-responsive encephalopathy associated with autoimmune thyroiditis (SREAT), linked to Hashimoto’s thyroiditis, show how brain-targeted autoimmunity can cause significant inflammation and cognitive challenges. This direct attack on the brain underscores why some autoimmune patients experience such pronounced neurological symptoms.
3. The Gut-Brain Axis: Inflammation Starts in the Gut
Your gut health plays a surprising role in brain function, and autoimmune diseases often disrupt the delicate balance of the gut microbiome. Gut dysbiosis, or an imbalance in gut bacteria, can trigger systemic inflammation that affects the brain, contributing to brain fog. Inflammatory foods like sugar, processed carbs, or gluten can worsen this by feeding harmful bacteria, which release inflammatory signals that reach the brain via the gut-brain axis.
Research on long COVID, which shares similarities with autoimmune conditions, suggests that gut microbiome changes may drive neuroinflammation and cognitive symptoms. A 2024 study found that microbiome dysfunction post-COVID was linked to brain fog, likely due to inflammatory cytokines affecting areas like the prefrontal cortex and limbic system.
4. A Leaky Blood-Brain Barrier: Letting Inflammation In
The blood-brain barrier (BBB) acts as a gatekeeper, protecting the brain from harmful substances. However, chronic inflammation in autoimmune diseases can make the BBB “leaky,” allowing inflammatory molecules, toxins, or autoantibodies to enter the brain. A 2024 study on long COVID patients with brain fog found evidence of a compromised BBB, which fueled neuroinflammation and cognitive issues. Similar mechanisms are at play in autoimmune conditions like lupus or multiple sclerosis, where immune cells, such as CD8 T cells, may damage the BBB and worsen brain inflammation.
5. Hormonal and Neurotransmitter Imbalances
Autoimmune diseases like Hashimoto’s thyroiditis can disrupt thyroid hormone levels, which are crucial for brain function. Low thyroid hormones are directly linked to brain fog and memory problems. Additionally, inflammation can throw off neurotransmitters like GABA or dopamine, leading to cognitive difficulties and reduced motivation.
For women, hormonal fluctuations—such as those during menopause—can compound brain fog, as estrogen plays a role in cognitive health. Chronic stress, common in autoimmune patients, also ramps up inflammation, further disrupting brain chemistry and worsening symptoms.
6. Cytokines: The Culprits Behind Cognitive Sluggishness
Inflammatory cytokines don’t just cause inflammation—they directly impair brain function. Studies show that cytokines like IL-6 and TNF reduce long-term potentiation (LTP), a process critical for learning and memory, and hinder neurogenesis, the creation of new brain cells. These effects manifest as brain fog, difficulty focusing, and even anhedonia (loss of pleasure). In autoimmune diseases, where cytokine levels are chronically elevated, these cognitive impacts can become persistent.
What You Can Do: Managing Brain Fog and Inflammation
The good news? By addressing the root causes of inflammation, you can take steps to reduce brain fog and support brain health. Here are research-backed strategies to consider:
1. Adopt an Anti-Inflammatory Diet
What to Eat: Focus on foods rich in omega-3 fatty acids (like salmon, walnuts, or fish oil), which reduce inflammation and support brain health. Include plenty of fruits, vegetables, and whole grains for antioxidants and fiber.
What to Avoid: Limit sugar, processed foods, and gluten, which can fuel inflammation and gut dysbiosis. An anti-inflammatory diet, like the Mediterranean diet, is a great starting point.
Why It Works: Dietary changes can lower systemic inflammation, improving cognitive function in conditions like long COVID and autoimmunity. Time after time, patients give anecdotal evidence of positive improvement with just diet modifications.
2. Support Gut Health
Incorporate probiotics and prebiotic foods (like kimchi, kefir, or fibrous veggies) to restore gut balance.
Consider working with a functional medicine practitioner to address gut dysbiosis, which can reduce systemic inflammation and its effects on the brain.
3. Balance Hormones and Stress
If you have an autoimmune condition like Hashimoto’s, ensure your thyroid hormones are optimized through medication and regular monitoring.
Manage stress with practices like meditation, yoga, or acupuncture, which lower inflammation and support neurotransmitter balance.
For women experiencing hormonal shifts, consult a healthcare provider about hormone-balancing strategies, as estrogen fluctuations can worsen brain fog.
4. Prioritize Lifestyle Changes
Exercise Regularly: Even moderate activity, like walking, boosts blood flow to the brain and reduces inflammation.
Sleep Well: Aim for 7–9 hours of quality sleep to support brain repair and lower cytokine levels.
Stay Hydrated: Dehydration can worsen cognitive symptoms, so drink plenty of water.
5. Explore Supplements
Glutathione: An antioxidant that reduces inflammation and supports detoxification.
Omega-3 DHA: Supports brain health and lowers neuroinflammation.
Vitamin D: Often low in autoimmune patients, it plays a role in immune regulation and cognitive function.
Consult a naturopath before starting supplements to ensure they’re safe for your condition.
The Research Gaps: What We Still Need to Learn
While science has made strides in understanding brain fog and inflammation, there are still challenges:
Brain fog isn’t well-defined, making it hard to study consistently. Researchers need clearer criteria to measure and treat it.
The roles of the blood-brain barrier and gut microbiome in autoimmune-related brain fog require larger, more robust studies.
Findings from long COVID research, while promising, may not fully apply to other autoimmune diseases, so more disease-specific studies are needed.
Take Control of Your Brain Health
Brain fog and brain inflammation can feel overwhelming, but understanding their roots in autoimmunity empowers you to take action. By addressing inflammation through diet, lifestyle, and medical support, you can clear the mental haze and improve your quality of life. If you suspect your autoimmune condition is affecting your cognitive health, talk to your healthcare provider about testing for inflammation markers, autoantibodies, or hormonal imbalances. Together, you can create a personalized plan to support your brain and body.
Reference:
Balter LJ, Bosch JA, Aldred S, Drayson MT, Veldhuijzen van Zanten JJ, Higgs S, Raymond JE, Mazaheri A. Selective effects of acute low-grade inflammation on human visual attention. Neuroimage. 2019 Nov 15;202:116098. doi: 10.1016/j.neuroimage.2019.116098. Epub 2019 Aug 12. PMID: 31415883.
Greene, C., Connolly, R., Brennan, D. et al. Blood–brain barrier disruption and sustained systemic inflammation in individuals with long COVID-associated cognitive impairment. Nat Neurosci 27, 421–432 (2024). https://doi.org/10.1038/s41593-024-01576-9
Dubey D, Pittock SJ, Kelly CR, et al. Autoimmune encephalitis epidemiology and comparison to infectious encephalitis. Ann Neurol 2018;83:166-177.