The Difference Between Hypothyroidism and Hashimoto’s

The terms hypothyroidism and Hashimoto’s are often used interchangeably, but they are not the same condition. Understanding the difference is essential, particularly if you are seeking effective, long-term support rather than symptom management alone.

At The Autoimmune Clinic, we support individuals who have been diagnosed with hypothyroidism without comprhensive investigations ,only to later discover that the underlying driver is autoimmune in nature. This distinction matters, because it influences how the condition develops, how it should be investigated, and how it is best supported.

What is Hypothyroidism?

Hypothyroidism refers to a state in which the thyroid gland is underactive and is not producing sufficient thyroid hormones to meet the body’s needs.

Thyroid hormones are critical for regulating metabolism, energy production, body temperature, digestion, mood and cognitive function. When levels are too low, a wide range of symptoms can develop.

Common symptoms of hypothyroidism include:

• Fatigue and low energy

• Weight gain or difficulty losing weight

• Cold intolerance

• Constipation

• Dry skin and hair thinning

• Low mood or depression

• Menstrual irregularities

• Brain fog and poor concentration

Hypothyroidism is a functional diagnosis based on low thyroid hormone output, but it does not specify why the thyroid is underactive.

In other words, hypothyroidism describes what the thyroid is doing, not what is causing it. Hypothyroidism can be temporary, hence moniroting thyroid function is important.

What is Hashimoto’s Thyroiditis?

Hashimoto’s thyroiditis is an autoimmune condition in which the immune system mistakenly attacks the thyroid gland.

Over time, this immune-mediated damage impairs the thyroid’s ability to produce hormones, which is why Hashimoto’s is the most common cause of hypothyroidism in the UK and other Western countries.

In Hashimoto’s:

• The immune system is the primary problem

• The thyroid is the target

• Hypothyroidism is the downstream result

Hashimoto’s can exist for many years before overt hypothyroidism develops. In fact, many individuals have autoimmune activity against the thyroid long before their standard thyroid markers become abnormal.

Key Differences Between Hypothyroidism and Hashimoto’s

Hypothyroidism	Hashimoto’s
Refers to low thyroid function	Refers to autoimmune disease
Describes hormone output	Describes immune attack
May have many causes	Specific autoimmune cause
Not always autoimmune	Always autoimmune
Treated with hormones	Treated with hormones (if needed) and requires immune-focused support

It is therefore entirely possible to:

• Have Hashimoto’s without overt hypothyroidism (yet)

• Have hypothyroidism that is not autoimmune in origin

Why the Distinction Matters Clinically

If hypothyroidism is treated without identifying whether it is autoimmune, the underlying immune dysfunction may remain unaddressed.

This is why many individuals:

• Continue to feel unwell despite being on levothyroxine

• Have fluctuating symptoms and unstable labs

• Develop additional autoimmune or inflammatory conditions over time

In functional and integrative medicine, identifying whether Hashimoto’s is present allows for a more targeted, preventative and systems-based approach.

How Are They Diagnosed?

Hypothyroidism is typically diagnosed using:

• TSH

• Free T4

• Sometimes Free T3

However, these tests alone do not identify autoimmune involvement.

Hashimoto’s requires additional testing:

• Thyroid Peroxidase Antibodies (TPO antibodies)

• Thyroglobulin Antibodies (TG antibodies)

A person can have:

• Normal TSH and T4

• But elevated antibodies

• And still have active autoimmune thyroid disease

This is one of the most commonly missed aspects of thyroid care in conventional settings.

Can You Have Normal Thyroid Labs But Still Have Hashimoto’s?

Yes, and this is very common.

Autoimmune activity against the thyroid often precedes changes in TSH and T4 by years. During this phase, individuals may already experience symptoms such as fatigue, anxiety, hair loss, weight changes and menstrual disruption, despite being told their thyroid is “normal”.

This is where a more comprehensive, root cause approach becomes particularly important.

What Drives Hashimoto’s?

Hashimoto’s does not arise in isolation. It reflects immune dysregulation influenced by a range of factors, including:

• Gut permeability and microbiome imbalance

• Chronic stress and nervous system dysregulation

• Infections

Environmental toxins and mould exposure

• Nutrient deficiencies

• Blood sugar instability

• Hormonal imbalances and transitions such as pregnancy and menopause

Supporting Hashimoto’s therefore involves much more than supporting the thyroid gland alone.

How Treatment Approaches Differ

Conventional management

In both hypothyroidism and Hashimoto’s, conventional medicine typically focuses on thyroid hormone replacement, most commonly levothyroxine.

While this can be necessary and appropriate, it does not:

• Address immune dysfunction

• Modify disease progression

• Reduce autoimmune activity

Functional medicine approach

At The Autoimmune Clinic, we consider:

• What is driving immune activation

• Why the thyroid has become a target

• Which factors are contributing to inflammation and autoimmunity

This allows for a more personalised strategy, particularly in individuals who:

• Remain symptomatic on medication

• Have multiple autoimmune or inflammatory conditions

• Have complex, multisystem presentations

How We Support Thyroid Health at The Autoimmune Clinic

We specialise in complex and immune-driven conditions, including Hashimoto’s thyroiditis and persistent hypothyroid symptoms.

Our approach includes:

• Comprehensive thyroid and autoimmune testing

• Functional interpretation of results

• Identification of dietary, lifestyle, immune, gut, hormonal, stress and environmental drivers

• Personalised nutrition, lifestyle and supplement strategies

• Collaboration with prescribing clinicians when required

If you suspect your thyroid issues may be autoimmune in nature, or if you are not improving despite treatment, we encourage you to explore a more comprehensive approach.

Keen to take the next step, book a call with Claire, our thyroid expert practitioner to discuss how she can help you.

Book a call with Claire