The Immunity–Hormone Connection: How Functional Medicine Practitioners Can Address Chronic Inflammation
by Dr. Dan Kalish
Understanding the Functional Medicine View of Inflammation
Chronic inflammation lies at the heart of nearly every modern health condition—from autoimmune disease to metabolic dysfunction, cognitive decline, and persistent fatigue. Yet, traditional lab testing rarely uncovers the why behind the inflammation.
In functional medicine, inflammation isn’t treated as a symptom—it’s seen as a sign of system-wide imbalance. At the Kalish Institute, we train practitioners to identify how the immune and endocrine systems interact, and how to use lab data to restore balance at the root level. Inflammation can be from emotional, dietary, GI/microbiome or toxin related factors. It’s complicated! Certainly, this immunity–hormone connection is one of the most important, and most overlooked, mechanisms driving chronic illness.
The Immunity–Hormone Connection Explained
Hormones are powerful immune modulators. They influence how the body responds to infection, stress, and injury—and, in turn, the immune system affects hormone signaling. When one system is out of sync, the other often follows.
Cortisol and the Stress–Inflammation Cycle
Chronic stress is one of the most common triggers of immune dysfunction. Dysregulation of the HPA axis elevates cortisol or flattens our diurnal rhythms, leading to immune suppression or a sustained pro-inflammatory state. Secretory IgA is at the heart of this immune response in it’s role in mucosal immunity. Fortunately, SIgA is easy to measure and track as a marker for mucosal immune health. High levels of SIgA indicate potential infection(s) and low levels tend to accompany a long term issue with our stress/survival response via cortisol.
Advanced testing such as DUTCH, HUMAP, Hormone Zoomer or salivary cortisol panels can identify these disruptions early, allowing practitioners to intervene before immune imbalance becomes chronic.
Thyroid Function and Immune Balance
Even mild hypothyroidism reduces metabolic efficiency, slows detoxification, and increases oxidative stress—all of which amplify inflammatory signaling. Testing Free T3, Free T4, TSH, and thyroid antibodies helps practitioners pinpoint metabolic bottlenecks that perpetuate inflammation.
Sex Hormones and Cytokine Regulation
Estrogen, progesterone, and testosterone shape immune tolerance and cytokine expression. Low progesterone or androgen deficiency can increase immune reactivity, while estrogen dominance may heighten autoimmunity risk. A DUTCH, HUMAP, Hormone Zoomer or serum hormone panel helps tailor interventions that calm immune activation and restore hormonal balance.
Cytokines and Feedback Loops
Inflammatory markers like IL-6, TNF-alpha, and CRP can dysregulate the endocrine system, creating a feedback loop of inflammation and hormonal disruption. Recognizing these loops early enables targeted, upstream solutions.
Using Functional Labs to Reveal Root Causes
Functional testing connects the dots between inflammation, hormone regulation, and metabolic health. The most useful assessments for practitioners include:
- HPA Axis/Cortisol/Adrenal Panels: Identify stress-related immune suppression or overactivation
- Thyroid Profiles: Reveal oxidative stress and metabolic sluggishness
- Sex Hormone Panels: Assess estrogen, progesterone, and testosterone balance
- Inflammatory Markers: Measure systemic stress with hs-CRP, cytokine panels, and oxidative metabolites
- Advanced Functional Testing: Organic acids, metabolomics, and microbiome testing to detect upstream drivers of fatigue and inflammation
Interpreted together, these results allow for precision, root-cause-driven interventions rather than symptomatic treatment.
Sequencing for Sustainable Results
Even with accurate lab data, outcomes depend on sequencing. The Kalish Method emphasizes phased interventions that align with the body’s physiology:
- Stabilize Hormones First – Balance cortisol rhythms and reduce acute inflammation through use of DHEA, pregnenolone, phos serine, licorice root, minerals and vitamins based on adrenal hormone test results as your first step in most treatment plans. Deal with thyroid and sex hormone imbalances up front as well.
- Repair the Gut Next – Heal the gut barrier, establish a healthy microbiome, eliminate GI infections after 2-3 months of lifestyle changes and HPA axis programs. Optimize detoxification, and restore key micronutrients that support hormone-immune balance.
- Detox Last – While often the most important treatment, detox is best left for when the lifestyle is in place for 3 months or more and the GI tract is working well. Address thyroid and sex hormone optimization to restore long-term resilience.
This structure helps practitioners achieve measurable, lasting change by supporting the body’s natural order of healing, starting by addressing lifestyle and survival/reproduction (i.e. stress and sex hormones). The true healing process lies far beyond lab markers and supplements as true healing depends on you (the healer) being healthy and vital yourself and having the patient be inspired by you. We suggest every practitioner start by testing themselves.
Translating Data Into Action
Let’s look at a common case: a patient with fatigue, high cortisol, low DHEA, mild hypothyroidism, and elevated CRP. Lab work shows low Free T3, high reverse T3, and elevated evening cortisol—clear indicators of HPA-axis stress.
Rather than targeting each issue separately, a systems-based approach integrates them: normalize cortisol patterns with DHEA, pregnenolone, adaptogens and circadian rhythm support; replenish thyroid cofactors such as selenium, zinc, and iodine; and reduce oxidative stress through antioxidant and mitochondrial support.
When reassessed 12 weeks later, improvements in energy, inflammation, and mood confirm what functional medicine does best—restore balance across systems.
How Kalish Institute Training Brings It All Together
The Kalish Institute equips practitioners to translate complex hormone and immune lab data into clear, actionable treatment plans. Our residency-style programs offer live lab interpretation, real case discussions, and mentorship from active clinicians who apply these methods daily. Our faculty, (I know this sounds scary) has an average of 33.75 years of clinical experience!
Practitioners learn how to:
- Integrate endocrine, immune, and metabolic data into one cohesive framework
- Sequence interventions for maximum physiological impact
- Communicate lab findings in ways that enhance patient engagement and adherence
This is where education meets clinical mastery—helping you deliver faster, more predictable results for your patients.
Ready to deepen your expertise in hormone and immune function?
Our intensive—Hormones & Immune Function—will explore these principles in depth. It’s part of the Kalish Longevity Certification, a program designed to give practitioners the lab-based strategies and communication tools to build personalized longevity protocols for their patients. ✨ Join us in redefining what it means to age well—both for your patients and your practice. ✨
