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Top 5 Differential Diagnosis for Abdominal Pain and How to Treat With Functional Medicine

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Top 5 Differential Diagnosis for Abdominal Pain and How to Treat With Functional Medicine

Abdominal pain is the most common gastrointestinal symptom reported in outpatient clinics (11). For patients receiving care for abdominal pain, an underlying cause cannot be determined in one-third of patients. The most common causes of abdominal pain are found to be gastroenteritis (7.2-18.7%), irritable bowel syndrome (2.6-13.2%), urological disease (5.3%), and gastritis (5.2%). 10% of patients with abdominal pain experience acute abdomen, which encompasses conditions that require urgent medical attention and treatment. Appendicitis, diverticulitis, gallbladder and pancreatic diseases, and cancer are responsible for the majority of acute abdomen. (1)

This article will discuss five of the most common causes of abdominal pain and briefly discuss the functional approaches to diagnosing and treating each.


How Common is Gastrointestinal Discomfort?

Abdominal pain is extremely common, with over 80% of people reporting pain in the outpatient setting. Despite these high numbers, two out of five people will not seek medical treatment for their symptoms. (11)

Why is a Differential Diagnosis Important for Abdominal Pain?

There are many reasons for abdominal pain that range from benign entities to life-threatening diseases. The abdomen houses many organs, all of which can be the reason for pain and other gastrointestinal symptoms. Constructing a broad differential diagnosis encompassing gastrointestinal, reproductive, cardiovascular, and urinary origins of pain ensures that potentially serious medical conditions causing symptoms are not missed.

Signs You Should See Your Physician

Signs warranting immediate and emergent medical attention include fever, persistent nausea and vomiting, blood in vomit or feces, and loss of consciousness.

Many times, abdominal pain is short-lived and doesn't require medical care. You should see your healthcare provider if gastrointestinal signs and symptoms persist for over a week and are unresponsive to over-the-counter remedies. Additionally, any sudden change in symptom quality warrants a medical evaluation.

Top Five Differential Diagnoses for Abdominal Pain

Abdominal pain can be caused by a wide range of conditions, so the differential diagnosis can be quite extensive. Here are some common differential diagnoses for abdominal pain:


Acute gastroenteritis is inflammation of the stomach, small intestine, and large intestine, most commonly caused by viral and bacterial pathogens. 179 million cases of gastroenteritis occur in the United States annually. Gastroenteritis is often referred to as "stomach flu," "traveler's diarrhea," and "food poisoning." The most common causative pathogens of gastroenteritis include rotavirus, norovirus, adenovirus, Salmonella, and Campylobacter.

Symptoms of Gastroenteritis

Gastroenteritis is a common cause of acute abdominal pain/discomfort, nausea, vomiting, diarrhea, and loss of appetite. It is usually self-resolving but can lead to dehydration when symptoms are severe. Pregnant women, the elderly, people with immunocompromise, infants, and premature babies are at higher risk for gastroenteritis complications. (4)

Stand Out Functional Medicine Labs for Gastroenteritis

Comprehensive Stool Test

The GI-MAP is a comprehensive microbiome analysis that uses PCR technology to identify over 50 bacterial, viral, parasitic, and fungal pathogens. It is a popular comprehensive stool test ordered by functional providers suspicious of infectious causes of gastrointestinal symptoms.

Functional Medicine Treatment for Gastroenteritis

Gastroenteritis is typically self-resolving, and treatment focuses on self-care measures to palliate symptoms and prevent dehydration. Sucking on ice chips and drinking water with added electrolytes will prevent electrolyte imbalances and draw water into the cells to support hydration. Resting the stomach with a short-term liquid fast with water or clear broths or following a BRAT diet can also reduce stomach pain and diarrhea. (10)

Antimicrobial herbs and probiotics can fight off viral and bacterial pathogens and reinoculate the digestive tract with healthy commensal bacteria. Probiotics are proven to reduce the duration of gastroenteritis symptoms and hospitalizations. Berberine-containing herbs like barberry, goldenseal, and Oregon grape have potent antidiarrheal and broad antimicrobial properties.

Irritable Bowel Syndrome (IBS)

IBS is a functional gastrointestinal disorder that affects up to 45 million people annually in the United States. It is characterized by recurrent abdominal pain associated with defecation or a change in bowel habits.

Symptoms of IBS

The predominant IBS symptoms are abdominal pain and disordered bowel habits (constipation and/or diarrhea). Abdominal bloating/distension and gas are also common. For an IBS diagnosis to be made, symptom onset must occur at least six months prior, and symptoms must be present for the last three months. (2)

IBS is classified into subtypes based on predominant bowel habits on days with abnormal bowel movements. IBS subtypes include IBS-constipation (IBS-C), IBS-diarrhea (IBS-D), and IBS-mixed (IBS-M).

Stand Out Functional Medicine Labs for IBS

SIBO Breath Test

Small intestinal bacterial overgrowth (SIBO) is commonly overlooked in the allopathic community but has been estimated to cause up to 80% of IBS. An at-home lactulose or glucose breath test measures gases produced by microorganisms colonizing the small intestine that are exhaled through the lungs. SIBO breath tests can diagnose the three subtypes of SIBO: hydrogen-SIBO, hydrogen sulfide-SIBO, and intestinal methanogen overgrowth (IMO).

Lactose Breath Test

Lactose intolerance is the presence of digestive symptoms after consuming lactose-containing foods due to a deficiency of the lactase digestive enzyme. Lactose intolerance symptoms are very similar to IBS symptoms. The most accurate and commonly utilized test to diagnose lactose intolerance is a breath test, which can be performed at home.

Food Sensitivities

Up to 65% of patients with IBS attribute their symptoms to adverse food reactions. A food sensitivity panel assesses for non-allergic immune reactions to foods, which are not commonly tested for by allopathic doctors but can cause IBS-like symptoms.

Thyroid Panel

Both hypothyroidism and hyperthyroidism can cause gastrointestinal symptoms that mimic IBS, including abdominal pain, constipation, and diarrhea. A complete thyroid panel measures all hormones involved in the thyroid hormone cascade. By looking at hormones produced by the brain and the thyroid and measuring thyroid antibodies, a complete panel allows for a comprehensive evaluation of how the body produces, processes, and utilizes thyroid hormones.  

Comprehensive Stool Test

The Gut Zoomer is a comprehensive stool test that measures biomarkers related to digestion, absorption, intestinal inflammation, and the gut microbiome. Comprehensive stool analyses offer extensive insight into malabsorptive, inflammatory, and dysbiotic imbalances that can contribute to IBS.

Functional Medicine Treatment for IBS

A functional approach to IBS addresses imbalances uncovered through functional medicine testing.

Dietary modifications are commonly recommended, including ensuring adequate fiber intake, avoiding high FODMAP foods, and therapeutic elimination diets based on food sensitivity testing results.

Functional medicine doctors routinely prescribe probiotics, prebiotics, antimicrobials, and prokinetic agents to address dysbiosis diagnosed with SIBO and stool testing.

Research shows a strong link between IBS symptoms and stress states (including anxiety and depression) attributed to the gut-brain axis. Mind-body medicine, including biofeedback, meditation, acupuncture, and yoga, focuses on the interactions between the mind and body to promote health. These modalities are proven to be effective in reducing IBS symptoms.

Kidney Stones

Kidney stones are crystal deposits formed inside the kidneys from different minerals and salts that concentrate in the urine. 12% of people globally will experience kidney stones at some point during their lives, with men and people with high blood pressure, diabetes, and obesity at a higher risk. The four main types of kidney stones are calcium oxalate, uric acid, struvite, and cystine.

Symptoms of Kidney Stones

Kidney stones cause symptoms as they travel through the kidney into the bladder. Small stones often don't cause any symptoms, but larger stones may become lodged in the ureters (the tubes that connect the kidneys to the bladder) and cause severe, sharp pain in the sides and back below the ribs that radiates to the lower abdomen and groin. The pain usually comes in waves and fluctuates in intensity. The pain is generally accompanied by urinary symptoms, including pain with urination, change in urine color (pink, red, or brown), cloudy or foul-smelling urine, and frequency and urgency. Nausea, vomiting, and fever may also occur. (3)

Stand Out Functional Medicine Labs for Kidney Stones

Kidney Function

Kidney function tests, including BUN, creatinine, and eGFR, are measured on a comprehensive metabolic panel (CMP) and give insight into how well the kidneys function.

A urinalysis is also routinely used to look for crystals, blood, bacteria, and white blood cells that may be present in the urinary tract with kidney stones in the acute scenario. For patients with recurrent stones, 24-hour urine collections that analyze calcium, oxalate, uric acid, citrate, sodium, and potassium are generally recommended to evaluate metabolic function and stone type (5).

Organic Acids

Organic acids are metabolic cellular byproducts that can be measured in the urine. Glyceric, glycolic, and oxalic acids measured on an organic acid test (OAT) are associated with an increased risk of kidney stone formation.

Functional Medicine Treatment for Kidney Stones

Kidney stone treatment recommendations depend on the type of stones the patient forms. All patients should increase their water intake to achieve a daily urine volume of at least 2.5 liters (5).

Dietary Recommendations for Kidney Stones

Patients with calcium stones and high urinary calcium output should limit sodium intake and consume 1,000-1,200 mg of calcium daily. Patients with low urinary citrate should increase their intake of fruits and vegetables and restrict non-dairy animal protein. (5)

Patients with calcium oxalate stones and high urinary oxalate output should limit oxalate-rich foods and maintain normal calcium consumption. (5)

Patients with uric acid or calcium stones with high urinary uric acid should limit their intake of non-dairy animal protein. (5)

Patients with cystine stones should limit sodium and protein intake to reduce cystine secretion. High fluid intake is essential in cystine stone treatment, and fluid intake of at least four liters daily is often recommended to decrease urinary cystine concentration. (5)

Supplements for Kidney Stones

Through oral supplementation or Epsom salt baths, magnesium can inhibit the formation of calcium oxalate stones (6).

Phyllanthus niruri, commonly known as stonebreaker, has been widely studied for its ability to block calcium oxalate crystallization and reduce oxalates and uric acid in the urine (6).


Gastritis is inflammation of the stomach lining most commonly caused by infection, autoimmunity, and NSAID and alcohol use.

Symptoms of Gastritis

Stomach upset and upper abdominal pain are the most common symptoms associated with gastritis. The pain is often associated with indigestion after meals. Other symptoms include:

  • Loss of appetite and increased fullness after meals
  • Nausea and vomiting
  • Heartburn and acid reflux
  • Bloating
  • Fatigue
  • Weight loss

If left untreated, gastritis can cause stomach ulcers, stomach bleeding, nutrient deficiencies, and in some cases, increase the risk of stomach cancer.

Stand Out Functional Medicine Labs for Gastritis

H. pylori

Helicobacter pylori (H. pylori) is the most common infectious agent of gastritis. Stool and breath testing are the most common and effective means for testing for H. pylori infection. A benefit of functional stool testing over conventional labs is the addition of antibiotic resistance testing that helps to guide treatment recommendations.


Autoimmune gastritis occurs when the body produces antibodies against parietal cells, which are responsible for making gastric acid. Not only can this autoimmunity cause gastritis, but it can also increase the risk for pernicious anemia, a common cause of vitamin B12-deficiency anemia.

Functional Medicine Treatment for Gastritis

An H. pylori eradication protocol should be initiated if the infection is diagnosed. Combo-therapy with prescription or natural antibiotics is recommended for all symptomatic patients with H. pylori. Commonly utilized natural agents for H. pylori eradication include mastic gum, licorice, sulforaphane, berberine, and lactoferrin. (7)

An anti-inflammatory diet that eliminates food intolerances and triggers like alcohol, coffee, and spicy and acidic foods and emphasizes plant flavonoids can reduce stomach irritation and protect the stomach lining. Supplements can be taken to support gastric healing, including L-glutamine, zinc carnosine, and aloe vera. (8)


Gallstones are pebble-like pieces of material that form in the gallbladder when the soluble components of bile become super-saturated and precipitate. Gallstones are usually made of cholesterol or bilirubin.

Symptoms of Gallstones

The majority of patients with gallstones do not have any symptoms. Acute symptoms will occur when a gallstone becomes lodged in the bile duct and causes an obstruction, called a gallbladder attack. Symptoms of a gallbladder attack may last minutes to hours and include:

  • Sudden and rapidly intensifying abdominal pain in the right upper abdomen and central abdomen below the breastbone
  • Radiating pain to the back between the shoulder blades and the right shoulder
  • Nausea and vomiting

Longstanding gallstones can lead to gallbladder inflammation, called cholecystitis. Cholecystitis can cause chronic abdominal pain, jaundice (yellowing of the skin), and clay-colored stools.

Stand Out Functional Medicine Labs for Gallstones

Hepatobiliary Function

A CMP includes biomarkers that assess liver and gallbladder function, including AST, ALT, alkaline phosphatase, and bilirubin. These markers are often elevated during gallbladder attacks or in patients with chronic gallbladder disease.

Cardiovascular Assessment

A cardiovascular assessment can benefit patients with gallstones, as diabetes, metabolic syndrome, and obesity can increase the risk of gallstone formation. An advanced lipid panel measures 15 lipid makers to analyze the risk of cardiovascular disease.

Hemoglobin A1c (HbA1c) and fasting insulin can be measured to assess blood sugar management and the risk of diabetes.

Comprehensive Hormone Panel

Women are twice as likely as men to develop gallstones because estrogen increases cholesterol and slows gallbladder emptying. The DUTCH test is a hormone panel that measures sex hormones and their metabolites to understand hormonal balance, metabolism, and their impacts on gallstone formation.

Functional Medicine Treatment for Gallstones

An anti-inflammatory diet with adequate dietary fiber and water intake prevents gallstone formation, facilitates cholesterol excretion from the body, and reduces gastrointestinal inflammation. (9)

Natural herbs and supplements commonly recommended to promote bile flow, stimulate healthy gallbladder muscle contractions, and dissolve gallstones include phosphatidylcholine, vitamins C and E, milk thistle, artichoke, dandelion root, and d-limonene (9).



Abdominal pain is a common concern that drives people to seek medical care in both outpatient and emergency settings. The differential diagnosis for abdominal pain is very broad, and all body systems must be considered when constructing a differential diagnosis. Gastroenteritis, IBS, gastritis, and conditions related to the urinary and hepatobiliary systems are common causes of abdominal pain. Acute abdomen requires emergent medical attention and usually conventional medical treatments. A functional medicine approach to abdominal pain searches for underlying causes to address chronic gastrointestinal symptoms and prevent the recurrence of acute medical conditions.

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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2. Lacy, B.E., & Patel, N. (2017). Rome Criteria and a Diagnostic Approach to Irritable Bowel Syndrome. Journal of Clinical Medicine, 6(11), 99.

3. Kidney stones - Symptoms and causes. (2022, June 3). Mayo Clinic.

4. National Library of Medicine. (2022, November 18). Gastroenteritis. MedlinePlus.

5. Pearle, M.S., Goldfarb, D.A., Assimos, D.G., et al. (2014). Medical Management of Kidney Stones: AUA Guideline. The Journal of Urology, 192(2), 316–324.

6. Weinberg, J.L. (2023, March 24). An Integrative Medicine Approach to Kidney Stones. Rupa Health.

7. Cloyd, J. (2023, March 20). A Functional Medicine H. Pylori Treatment Protocol. Rupa Health.

8. Weinberg, J.L. (2023, March 2). An Integrative Medicine Approach to Gastritis. Rupa Health.

9. Weinberg, J.L. (2023, March 2). These Lifestyle Choices Increase Your Risk Of Gallstones. Rupa Health.

10. Viral gastroenteritis (stomach flu) - Diagnosis and treatment. (2022, January 18).

11. Lakhoo, K., Almario, C.V., Khalil, C., et al. (2021). Prevalence and Characteristics of Abdominal Pain in the United States. Clinical Gastroenterology and Hepatology, 19(9), 1864-1872.e5.

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