Most people think of Rheumatoid arthritis as a joint condition. They picture swollen fingers, stiff hands and aching knees, as though the story begins and ends in the cartilage.
But in reality, rheumatoid arthritis is a systemic autoimmune disease first and a joint disease second.
By the time joints become visibly inflamed, the immune system has often been dysregulated for months — sometimes years.
Long before I ever worked clinically in autoimmunity, and long before I had the language or the training to understand what was happening in my body, there were signs that something deeper wasn’t right. I had already experienced alopecia from the age of seven and grew up with ongoing skin issues, so in many ways immune dysregulation had always been part of my story. Yet when my joints began to ache and swell years later, no one ever connected those dots.
My energy was persistently flat no matter how well I slept, my digestion was inconsistent, and I moved through long phases of feeling inflamed without being able to explain why. At the same time, my knuckles would swell for no obvious reason and small ganglion cysts would appear on my wrists and fingers. My hands often felt sore and stiff, almost as though I had overused them, even on days when I hadn’t done anything strenuous. There was a tenderness that didn’t quite make sense.
But every time I sought answers, the tests came back “normal”. I was told it was probably tendonitis. Or overuse. Or stress.
Even though I had a clear history of autoimmune issues, even though there was swelling, ganglions, fatigue and systemic symptoms, it was treated as a local, mechanical problem rather than an immune one.
So I learned to minimise it, like so many people do. Yet intuitively I knew this wasn’t just wear and tear. It felt systemic. It felt inflammatory. It felt like my body was trying to tell a bigger story that no one was quite listening to.
Years later, when I finally focused on repairing my gut and calming my immune system properly, those joint symptoms quietly disappeared alongside everything else. The swelling stopped, the ganglions never came back, and my hands simply felt normal again.
That was the moment it truly clicked for me that rheumatoid and autoimmune symptoms rarely start in the joints. They start in the terrain underneath.
And the joints are often just where the story becomes visible.
Before we dive in, if you’d like to explore this topic more deeply, I recently recorded an episode of The Autoimmune RESET Podcast where I talk through rheumatoid arthritis, the early symptoms people often miss, the root causes we see clinically, and the natural therapies I use in practice. It’s called Rheumatoid Arthritis: Symptoms, Root Causes and Natural Therapies, and it’s a lovely companion to this article.
1. Persistent fatigue that doesn’t improve with rest
One of the earliest symptoms of rheumatoid arthritis is often profound fatigue, yet it is rarely recognised as inflammatory.
This isn’t simply being busy or under-slept. It’s the kind of tiredness that feels cellular, as though your body has quietly turned the dimmer switch down on your energy.
Inflammatory cytokines associated with RA, such as IL-6 and TNF-alpha, can interfere with mitochondrial energy production. In simple terms, your cells make less ATP, so everything feels harder than it should.
Many of my clients describe this phase as feeling “not quite themselves” long before any joint pain appears.
2. Digestive issues, bloating, or IBS-type symptoms
If there is one connection I wish more people understood, it’s the relationship between gut health and autoimmune disease.
Around seventy to eighty percent of the immune system lives in the gut. When the microbiome becomes imbalanced or the intestinal lining becomes more permeable, the immune system becomes reactive and confused. Over time, this can contribute to chronic inflammation and, in some people, the production of antibodies linked with rheumatoid arthritis.
Bloating, food sensitivities, constipation, loose stools or a long-standing IBS diagnosis are incredibly common in people who later develop RA.
When I finally focused on repairing my own gut barrier and restoring microbial balance, my joint symptoms improved alongside my digestion. It was one of the clearest cause-and-effect experiences of my career.
3. A low-grade “flu-like” or inflamed feeling
Many people describe this symptom but struggle to name it.
They don’t feel acutely ill, yet they don’t feel well either. There’s a vague achiness, a slightly feverish quality, or the sense that the body is fighting something in the background.
This reflects systemic inflammation, not just local joint irritation. It is often one of the immune system’s earliest whispers, long before swelling becomes visible.
4. Brain fog, anxiety, or disrupted sleep
Because rheumatoid arthritis is inflammatory, it doesn’t stay politely in one part of the body.
Inflammatory messengers cross into the brain and influence neurotransmitters, cortisol rhythms and vagal tone. This is why cognitive and mood changes are surprisingly common early symptoms.
Poor focus, low mood, light sleep, or that wired-but-tired feeling can all be part of the same physiological picture.
For years I thought this was simply stress. In hindsight, it was immune activation.
5. Subtle joint changes that come and go
Ironically, even the “joint symptoms” don’t always look dramatic at first.
In my case it was intermittent swelling in the knuckles, stiffness in the mornings and small ganglion cysts that appeared and disappeared. Because they weren’t constant, they were easy to ignore.
But they were likely early immune irritation rather than wear and tear.
And once the inflammation settled, they simply stopped happening.
What markers do we test for in Rheumatoid Arthritis?
Clinically we often assess:
- Rheumatoid Factor (RF)
- Anti-CCP / anti-citrullinated protein antibodies
- CRP and ESR
- Iron, vitamin D, thyroid markers
- plus deeper gut and microbiome testing
If RF or anti-CCP are positive, it’s important to take note, as these antibodies can be associated with more aggressive disease.
However, some people have clear symptoms with negative blood tests. This is known as seronegative rheumatoid arthritis, and it’s one of the reasons why symptoms and clinical history matter just as much as lab results.
A normal test doesn’t automatically mean nothing is happening.
Where I always start: gut health first
Because the immune system is so intimately linked to the gut, this is nearly always my first therapeutic focus.
Stabilising blood sugar, increasing protein, prioritising omega-3 fats, improving sleep, reducing ultra-processed foods and actively supporting the gut barrier can make a surprisingly profound difference.
When appropriate, I use comprehensive gut testing to understand dysbiosis and inflammation patterns, and I often recommend Symprove, a liquid probiotic designed to reach the gut alive. They’ve offered 50% off with code AN50 at checkout (the last page), which can be a simple place to begin.
Because sometimes the most meaningful improvements don’t come from chasing the joints.
They come from calming the terrain underneath them. It certainly did for me.
You can learn more about the comprehensive gut testing that is offered at the Autoimmune Nutrition Clinic here.
Which gut test is right for you?
One of the questions I’m asked almost daily is which gut test to choose, especially when people start to understand how intimately gut health and autoimmunity are linked.
Because if the immune system largely resides in the gut, then it makes sense to look there first rather than guessing.
In clinic, stool testing often gives us the missing pieces. It helps us see whether inflammation, dysbiosis, infections, poor digestion or barrier issues are quietly driving immune activation in the background. And for many people with rheumatoid symptoms, fatigue, skin flares or other autoimmune patterns, this is where the real leverage lies.
Below is how I typically guide clients.
“Do I really need a stool test?”
Not everyone does, but if you have ongoing digestive symptoms, autoimmune disease, unexplained inflammation, food sensitivities, or symptoms that don’t match your blood work, it can be incredibly illuminating.
It allows us to stop guessing and start being precise.
“What’s the difference between GI Effects and Microbiome Explorer?”
Both are excellent tests. They just answer slightly different questions.
GI Effects — comprehensive function and pathogens
This is the test I often choose when we want a broad, clinical overview.
It looks at:
- digestion and enzyme output
- inflammation markers
- short-chain fatty acids
- parasites, bacteria, yeast
- gut immune markers
- microbiome balance
It’s particularly useful if someone has clear IBS-type symptoms, bloating, loose stools, constipation, or suspected infections or overgrowths. It gives us both functional and microbial data, so it’s very actionable.
Microbiome Explorer — deeper microbiome mapping
This test goes deeper into microbial diversity and patterns, using more advanced sequencing.
It’s brilliant when we’re focusing on:
- immune regulation
- Autoimmunity
- Children
- subtle dysbiosis
- long-term terrain work
I often use this for clients with alopecia, eczema, autoimmune disease or chronic inflammatory issues where the picture is less about infection and more about overall ecosystem balance.
If GI Effects shows us what’s “wrong”, Microbiome Explorer often shows us what’s “missing”.
Both perspectives can be valuable — it just depends on the clinical story.
“Which one would you choose for me?”
In practice, this doesn’t need to feel complicated.
If your symptoms are primarily digestive — bloating, constipation, loose stools, reflux, food reactions, or suspected infections or overgrowth — I usually recommend GI Effects or GI360. These are comprehensive functional stool tests that look at digestion, inflammation, pathogens, enzymes and the overall health of the gut environment. They’re incredibly practical and give us very actionable data.
If your symptoms feel more immune or systemic — things like autoimmunity, hair loss, skin flares, fatigue, or long-standing inflammatory patterns where the gut picture is subtler — I often prefer Microbiome Explorer, which looks more deeply at microbial diversity and ecosystem balance. It helps us understand the terrain, not just what’s “wrong”.
Both are tests I use regularly in clinic, and both can be ordered directly through The Autoimmune Nutrition Clinic website, so you can get started straight away.
GI Effects and GI360 are available across the UK, US (excluding New York), and Europe.
Microbiome Explorer is currently available in the UK and Europe only.
So wherever you’re based, there’s a clear next step.
VJ Hamilton, BSc, RNT
VJ Hamilton is a Registered Nutritionist (BANT) and an expert in autoimmune disease. VJ combines her knowledge from her medical science degree in Biochemistry & Immunology with Nutritional Therapy to offer a thorough and personalised approach to support her clients based on the most current scientific research. VJ runs a virtual and in-person nutritional therapy and functional medicine practice, The Autoimmunity Nutritionist, specialising in gut skin and immune health.