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A Functional Medicine Interstitial Cystitis Protocol: Testing, Nutrition, and Supplements

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A Functional Medicine Interstitial Cystitis Protocol: Testing, Nutrition, and Supplements

Interstitial cystitis is a chronic pain disorder with an estimated prevalence of 3-8 million women and 1-4 million men in the United States. However, these numbers may be underestimated given the difficulties associated with diagnosis and underdiagnosis, especially in men. (17

Given the complexity of interstitial cystitis, research suggests that a multimodal, integrative treatment plan, including diet therapy, stress management, and physiotherapy, can lead to treatment success rates of over 90%. This article will discuss a functional medicine approach to interstitial cystitis and provide a sample treatment plan that can be implemented in clinical practice.


What is Interstitial Cystitis?

Interstitial cystitis (IC) is also known as painful bladder syndrome (PBS) and bladder pain syndrome (BPS). It is a chronic pelvic pain condition characterized by recurring urinary urgency and frequency and bladder pain or pressure in the bladder and pelvic region, lasting at least six weeks without infection or other clear cause. IC affects millions of men and women but is most common in women in their 30s or older. (24

Interstitial Cystitis Signs & Symptoms

The signs and symptoms of interstitial cystitis (IC) can vary among individuals, and some people may experience periodic remissions and flare-ups. Common signs and symptoms of IC mimic those of a urinary tract infection (UTI) (17): 

  • Pelvic pain or discomfort ranging from mild to severe and described as an aching, pressure, or burning sensation in the pelvic region and the bladder. This sensation is worsened by filling the bladder and is often relieved by urinating.
  • Urinary frequency and urgency: feeling the need to urinate more often than usual and urgently, even when the bladder is not full. Patients often wake frequently during the night to urinate (nocturia). 
  • Painful urination (dysuria): urinating is accompanied by pain or a burning sensation
  • Pain during sexual intercourse (dyspareunia) 

IC can lead to various complications that can significantly impact a person's quality of life. These complications may include chronic pain, sleep disturbances due to nocturia, emotional distress such as anxiety and depression, and decreased sexual intimacy and satisfaction. Additionally, the chronic nature of IC and the constant need to manage symptoms can lead to limitations in daily activities, work productivity, and social interactions. (13)

What Causes Interstitial Cystitis?

The exact cause of interstitial cystitis (IC) remains unknown, and it is believed to be a multifactorial condition with various contributing factors leading to inflammation. 

One possible cause is a disruption in the bladder's protective lining, known as the urothelium, which can make the bladder more susceptible to irritation and inflammation. When the urothelium is healthy, it acts as a barrier, preventing irritating substances in the urine from directly contacting the underlying bladder tissue. However, the urothelium may become compromised in individuals with IC, leading to increased permeability or "leakiness." A leaky urothelium allows toxins, bacteria, and inflammatory mediators to penetrate the bladder tissue, leading to chronic bladder inflammation and irritation. (17)  

Furthermore, dysregulation of the immune system has been implicated in IC. It is thought that an autoimmune response or chronic low-grade inflammation in the bladder may contribute to the development and progression of the condition. Immunoglobulin and immune mediators are detected at higher levels in the urine of affected individuals. A growing body of evidence suggests a correlation between IC and histamine intolerance, as histamine released during an immune response can contribute to bladder inflammation and trigger IC symptoms in susceptible individuals (15). (17

Ongoing research is exploring the connection between the urinary microbiome and IC. Traditionally, urine was believed to be sterile, but recent studies have shown that the urinary tract contains a diverse microbial community. In individuals with IC, imbalances or dysbiosis in the urinary microbiome have been observed, potentially contributing to the development or worsening of IC symptoms. It is hypothesized that these microbiome alterations may trigger chronic inflammation and immune responses in the bladder; specific microorganisms within the urinary microbiome could directly irritate the bladder or disrupt its normal function. (2

Other factors contributing to IC include pelvic floor dysfunction, nerve abnormalities, and lifestyle factors such as diet and stress. Pelvic floor dysfunction can increase tension or weakness in the pelvic muscles, leading to bladder dysfunction and pain. Nerve abnormalities in the urinary system can disrupt the communication between the bladder and the brain, contributing to IC symptoms. Moreover, dietary triggers such as acidic foods, caffeine, artificial sweeteners, alcohol, and other food sensitivities may exacerbate IC symptoms in some individuals. Psychological stress can also worsen symptoms, as the stress response can affect the immune system and trigger inflammation. (1

Functional Medicine Labs to Test for Root Cause of Interstitial Cystitis

IC remains challenging to diagnose given the lack of a definitive diagnostic test to determine its presence; therefore, it remains a diagnosis of exclusion, meaning that other diagnoses must be excluded first before landing on IC as the cause of symptoms. A comprehensive patient history confirming the presence of symptoms for at least six weeks, a thorough physical exam, and negative urine culture should be obtained to make an IC diagnosis.

Although there isn't a definitive test to rule in the diagnosis, many specialty labs can assist in uncovering the underlying imbalances contributing to urinary inflammation and symptoms. 

Microbiome Testing

While urinary microbiome testing is not readily available, research suggests that the gastrointestinal microbiota may influence the urinary tract (5). Additionally, gastrointestinal dysbiosis is known to contribute to immunological dysfunction, contributing to systemic inflammation and hyperreactivity. A stool test collected at home by the patient can assess the patient's complete gut microbiome and function. 

SIBO Breath Test

In a 12-year cohort study, irritable bowel syndrome (IBS) increased the risk of developing IC. The study found that, on average, it took approximately five years from diagnosing IBS to developing IC. Additionally, these results suggest that shared common factors may contribute to the development of both conditions. 

Studies suggest that up to 80% of people with IBS have small intestinal bacterial overgrowth (SIBO), contributing to their digestive symptoms (6). A SIBO breath test measures gaseous byproducts derived by intestinal microbes to diagnose and differentiate between the various SIBO subtypes. 


Histamine is a chemical compound involved in immune responses, inflammation, and allergic reactions. Studies have observed increased expression of histamine receptors in bladder tissue samples retrieved from patients with IC and that antihistamines improve IC-related pelvic pain. Measuring histamine can help assess histamine intolerance as a contributor to bladder inflammation and assist in monitoring treatment effectiveness.

Food Sensitivities

Research reveals that patients with IC have significantly more food sensitivities than those without. Some studies indicate that as many as 90% of patients with IC report food sensitivities (5). A comprehensive panel that measures immune-mediated reactions to common food allergens can help identify dietary-related IC triggers and refine therapeutic dietary modification recommendations.  

Hormone Panel

IC symptoms in women often fluctuate with hormonal changes, with some experiencing their first symptoms during perimenopause or menopause. This connection is likely linked to estrogen levels. A decrease in estrogen can activate mast cells, so many women may begin to experience IC symptoms leading up to menopause. Furthermore, inflammation, mast cell activity, and estrogen affect the bladder lining and detrusor muscle, potentially causing thinning, dryness, and increased susceptibility to inflammatory changes. Restoring hormonal balance becomes crucial in reducing the susceptibility to IC. A hormone panel can help identify and correlate hormonal imbalances with IC symptoms throughout the various phases of the menstrual cycle. (1


Conventional Treatment for Interstitial Cystitis

Conventional treatment options for IC aim to alleviate symptoms, reduce inflammation, and improve bladder function. These treatments are often prescribed based on the severity of symptoms and may involve a combination of therapies. First-line treatments typically include lifestyle modifications and dietary changes. Patients are advised to avoid potential trigger foods such as acidic and spicy foods, caffeine, alcohol, and artificial sweeteners. Bladder training techniques, which involve gradually increasing the time between urinations, may also be recommended to improve bladder capacity and reduce urgency. (17

Medications play a significant role in managing IC symptoms. Oral medications such as nonsteroidal anti-inflammatory drugs (NSAIDs), antihistamines, and tricyclic antidepressants (TCAs) can help alleviate pain, reduce inflammation, and improve sleep quality. Additionally, bladder-instilled medications, such as pentosan polysulfate sodium (PPS) or lidocaine, may be administered directly into the bladder to provide localized relief. (10, 17)

More invasive procedures may be considered for individuals with severe IC symptoms that are unresponsive to other treatments. These can include bladder distention, where the bladder is filled with fluid to stretch the bladder wall and reduce pain signals, or neuromodulation techniques, such as sacral nerve stimulation or botulinum toxin injections, which aim to regulate nerve signaling and improve bladder function. (1, 17)

Functional Medicine Treatment Protocol for Interstitial Cystitis

Functional medicine approaches the treatment of IC by addressing the underlying causes through a personalized approach. This may involve dietary modifications to reduce inflammatory triggers, stress management techniques, addressing imbalances in the microbiome through probiotics or other interventions, and targeted therapies to support bladder health and immune function. By identifying and addressing the root causes specific to each individual, functional medicine aims to alleviate symptoms and improve overall bladder health in those with IC.

Therapeutic Diet and Nutrition Considerations for Interstitial Cystitis

Therapeutic dietary modifications play a crucial role in managing the symptoms of IC. While there is no one-size-fits-all diet for IC, certain nutritional changes have shown promise in reducing bladder irritation and alleviating symptoms. (11, 20)

One essential dietary modification for IC is avoiding potential trigger foods. These can vary among individuals, but common triggers include acidic foods (such as citrus fruits, tomatoes, and vinegar), spicy foods, caffeine, alcohol, artificial sweeteners, and foods high in potassium or histamine. Food sensitivity testing can also guide dietary eliminations. An elimination diet is often performed for at least 2-4 weeks to observe if IC symptoms improve. Keeping a food diary and tracking symptom triggers can help identify specific foods that worsen symptoms. (1

Another dietary approach is the IC diet, which focuses on consuming bladder-friendly foods less likely to irritate the bladder. This typically includes low-acid foods like pears, apples, green vegetables, lean proteins, whole grains, and non-citrus juices. 

Supplements Protocol for Interstitial Cystitis

Supplements can be used as natural alternatives to or in conjunction with prescription medications to relieve pain and correct the underlying imbalances contributing to bladder inflammation. A supplement protocol that specifically targets an individual's IC triggers, based on laboratory findings, should be prescribed. Below is a sample protocol that could be considered.

N-Acetyl Glucosamine

Glycosaminoglycans (GAGs) are naturally occurring substances contributing to the protective urothelium. GAG supplementation aims to restore and support the integrity of the urothelium to reduce bladder irritation. Clinical studies have shown that GAG supplementation can improve urinary symptoms, decrease pain, and enhance bladder capacity in some individuals with IC.

Dose: 500 mg three times daily

Duration: 6-12 months


Kava (Piper methysticum) is known historically as a urinary antispasmodic and anti-inflammatory agent. Moreso, it can be used as a natural anxiolytic agent, helpful in IC cases reported to be aggravated by stress, or to support the general emotional well-being of patients. 

Dose: 70 mg kavalactones three times daily

Duration: as needed for pain and anxiety


Arginine is an amino acid that plays a role in various physiological processes, including wound healing and immune function. Some individuals with IC may consider arginine supplementation due to its potential vasodilatory effects and its involvement in nitric oxide synthesis, which can impact bladder function. Although evidence is limited, several studies have reported positive benefits of L-arginine supplementation in treating IC. For example, one study reported increased urinary nitric oxide-related enzymes and metabolites with long-term L-arginine supplementation; this result correlated with decreased IC symptoms.

Dose: 500 mg three times daily

Duration: 6 months


Quercetin is a flavonoid with antioxidant and anti-inflammatory properties. It modulates the immune response and inhibits the release of histamine and other inflammatory mediators from mast cells. This small study showed that just four weeks of quercetin supplementation safely improved IC urinary symptoms and pain scores.

Dose: 500-1,000 mg twice daily

Duration: at least four weeks

When to Retest Labs

Correcting the underlying imbalances associated with IC symptoms often takes time; therefore, functional medicine practitioners don't expect to see changes reflected in specialty labs immediately after starting a treatment protocol. Labs are often reordered between 3-6 months from baseline to assess the patient's response to treatment. 

Learn More About Interstitial Cystitis



Interstitial cystitis can cause debilitating bladder and pelvic pain for affected individuals. The complexity of the condition, along with a lack of definitive diagnostic testing available, makes the condition underdiagnosed and difficult to manage. Conventional medical guidelines for treatment call for a multifaceted approach to effectively manage symptoms and improve patients' quality of life. Functional medicine has the upper hand, using specialty tests to pinpoint the underlying pathophysiology contributing to bladder irritation and inflammation. Using an integrative treatment approach, as outlined in this article, achieving a pain-free life is possible. 

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article

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