Imagine you have been working with an especially complex GI patient in your practice. They are experiencing bouts of bloating, early satiety, and erratic bowel habits. Over the course of multiple visits, you order an upper endoscopy, a colonoscopy, an abdominal CT, and routine serum panels. However, all test results come back completely normal. There is no smoking gun, and you are left right where you started: scratching your head in confusion.
The complex GI patient who doesn’t get better is actually a common phenomenon. The reason lies in the way we go about investigating gut health issues. Conventional gastroenterology is built to identify acute conditions—specific malignancies, ulcerations, active IBD flares—leaving functional and systemic issues undetected.
The problem with this approach is that it doesn’t deal with digestion as it really exists in the body: an interconnected system. When one component fails, every other component inevitably breaks down. Treating individual symptoms while failing to account for the systemic nature of the GI is what keeps these complex patients sick.
Upstream Failure: The Hypochlorhydria Paradox
Let’s take a look at heartburn and reflux as instructive examples. What does conventional gastroenterology prescribe for these ailments? Antacids to weaken stomach acids.
In reality, these are most often symptoms of insufficient gastric acid (hypochlorhydria) rather than too much acid (hyperchlorhydria). While perhaps counterintuitive, it makes sense when you consider digestion as a system:
- Hypochlorhydria impairs the stomach’s ability to break down ingested protein into smaller pieces.
- This undigested food sits in the stomach longer than normal and begins to ferment.
- Fermentation creates gases and builds up pressure inside the stomach.
- The upward pressure physically forces the valve at the top of the stomach open, splashing acid upward into the esophagus and irritating the sensitive throat.
As a result, people assume they have "too much acid." But the real problem is that their stomach isn't breaking down food—something no amount of antacids will fix!
Clinical training covers reflux, IBS, inflammatory bowel disease, and celiac disease, each with its own diagnostic criteria and drug. Yet that training rarely covers the assessment sequence that tells you where to begin when a patient presents with overlapping complaints and a chart full of unremarkable results.
As a result, the complex GI patient is left to suffer years of chronic symptoms, escalating dietary restrictions, and appointments that end without answers.
But it doesn’t have to be this way.
In the latest Kharrazian Institute Master Class, "Digestive Assessment for Complex Cases," Dr. Liz Lipski teaches a digestive assessment that works. The key is following a structured order:
- How the patient digests and absorbs food
- Whether the gut barrier is intact
- What the microbiome is doing
- Where inflammation is located
- How the nervous system drives it all
Skip that order, and you are selecting interventions by guesswork. Follow it, and you can start to give health back to your most challenging GI patients.
Click here to learn more about this exciting new KI Master Class and register today.
Downstream Collapse: Brush Border Erosion and Endotoxemia
The havoc caused by undigested food in the GI doesn’t stop at acid reflux or heartburn. When food isn't broken down properly upstream, large food particles and overgrown bacteria enter the small intestine, where they cause constant friction against the single-cell mucosal lining. This chronic irritation wears down the gut’s brush border (the velvet-like absorbing surface) and damages tight junctions.
As those tight junctions loosen, microscopic gaps open up in the intestinal wall. Toxic debris shed from common gut bacteria—known as lipopolysaccharides (LPS)—slips through these gaps and leaks directly into the bloodstream, leading to endotoxemia.
Worse yet, the liver's natural filtration system quickly gets overwhelmed by this steady influx of gut-derived toxins. This causes immune reactions across the entire body. What started as an isolated digestive issue in the stomach transforms into widespread inflammation, persistent brain fog, aching joints, chronic fatigue, and skin flare-ups.
Why does one patient recover on a protocol while another sees no change? Dr. Liz Lipski has spent her career answering that question. Her secret?Assessing digestion in sequence rather than by symptom label.
In Dr. Lipski’s latest course, "Digestive Assessment for Complex Cases," she distills that sequence into something you can apply in your next appointment. The course covers digestive and absorptive capacity; intestinal permeability and bacterial LPS; microbiome composition and its dietary modulation; inflammation and immune activation; and the enteric nervous system, which determines whether any of it holds. Plus, you’ll learn the intake tool she developed to stratify digestive priorities and track changes over time.
You’ll get access to all of this and more when you register for this Master Class. Click here to get started.
Misdiagnosed PEI: The Hidden Pancreatic Driver
The pancreas is another culprit of GI issues that the conventional approach often misses. Exhibit A is pancreatic exocrine insufficiency (PEI), which is frequently mislabeled as diarrhea-predominant or mixed IBS (IBS-D/IBS-M). But why?
For one, the signs of PEI are indistinguishable from IBS based on symptoms alone. Patients typically present with general complaints such as gas, bloating, stomach pain, mild abdominal discomfort, watery diarrhea, and weight loss. Because these symptoms are nonspecific and IBS is a natural starting point for diagnosis, PEI can be misidentified and therefore left unchecked for years.
PEI is also frequently comorbid with conditions like Crohn’s disease, celiac disease, and SIBO. These overlapping issues can mask underlying pancreatic dysfunction too. And when these comorbidities are present, conventional fecal fat testing—which is used to detect pancreatic insufficiency—can yield ambiguous or unclear findings. This leads to further misidentification issues.
Additionally, clinicians often rely on symptom checklists rather than ordering a fecal pancreatic elastase test. This test provides an objective enzyme measurement that, when low, can signal pancreatic insufficiency. When this simple stool marker is not evaluated, the enzyme deficiency remains hidden, usually beneath an IBS diagnosis.
Introducing "Digestive Assessment for Complex Cases" by Dr. Liz Lipski
The "normal test results, sick patient" narrative is all too common in clinics today. It stems from viewing digestion issues as a series of siloed symptoms, rather than viewing the GI tract as an interconnected system where a single issue could have wide-ranging, seemingly unrelated effects. But when we change our view of digestion to match how our bodies actually work, we begin to change how we process symptoms, order tests, and ultimately treat our complex GI patients.
In "Digestive Assessment for Complex Cases," Dr. Liz Lipski teaches clinicians how to step back from symptom whack-a-mole and systematically map complex GI cases. Dr. Lipski distills three decades of clinical practice into a working sequence of thought for digestive assessment. When you register for the course, you will learn to:
- Organize a patient's digestive priorities before ordering a single test
- Interpret gastric acid status when symptoms point in two directions at once
- Select the stool testing methodology that answers the question you are actually asking
- Match a therapeutic elimination diet to a diagnosis rather than to a hunch
Every recommendation is anchored in published research, comparative laboratory data, and cases in which conventional testing returned normal results while the patient continued to decline.
Liz Lipski holds a PhD in Clinical Nutrition from the Union Institute and is a Fellow of the American College of Nutrition (FACN). She holds dual board certifications in clinical nutrition (CNS and BCHN), is certified in functional medicine (IFMCP), and is a Cochrane member. Dr. Lipski retired in 2022 as Professor and Director of Educational Development for the Nutrition programs at Maryland University of Integrative Health. She continues to teach in the Gastrointestinal Modules at the Institute for Functional Medicine.
Frequently Asked Questions
How can a patient have normal test results while still experiencing severe GI symptoms?
Standard gastroenterology tests are designed to spot acute conditions, such as ulcers, tumors, or IBD. These tests rarely measure functional or systemic deficits.
Why are heartburn and reflux often caused by hypochlorhydria as opposed to hyperchlorhydria?
When stomach acid levels are too low (hypochlorhydria), the stomach cannot efficiently break down ingested protein. This undigested food stays in the stomach longer than it should and begins to ferment, generating gas and building up internal pressure. That upward pressure physically forces open the valve at the top of the stomach, splashing acid up into the esophagus and throat.
How do I clinically differentiate pancreatic exocrine insufficiency (PEI) from standard IBS-D or IBS-M?
Because PEI and IBS share overlapping symptoms like bloating, abdominal discomfort, and loose stools, relying on symptom checklists alone often leads to misdiagnosis. Fecal fat testing can also be inconclusive, especially in the presence of comorbidities like SIBO or celiac disease. The most reliable way to screen for hidden PEI is by ordering a fecal pancreatic elastase test, which provides a direct, objective measurement of exocrine pancreatic output.
How can I learn to systematically sequence assessment and protocol design for GI patients?
To stop relying on diagnostic guesswork and start mapping complex cases with confidence, enroll in Dr. Liz Lipski’s new Kharrazian Institute Master Class, "Digestive Assessment for Complex Cases." In this course, Dr. Lipski shares her proven sequence for evaluating digestion, intake stratification tools, and practical methods to interpret ambiguous labs. Click here to learn more, register, and transform your clinical approach to complex GI care.
