Hidden Root Causes of Chronic Constipation

Every day, I meet clients who are finally ready to take control of their constipation. Many have been handed a diagnosis like IBS-C (Irritable Bowel Syndrome, Constipation-Dominant) or “Functional Constipation” and sent home with laxatives and vague advice: eat more fiber, move more, drink more water. While these tips are helpful, they rarely get to the root of the problem.

The truth? Chronic constipation almost always has an underlying—and treatable—cause. And if we don’t address that, we’re just managing symptoms, not solving the issue.

This post is for anyone who’s been labeled with IBS-C or Functional Constipation (or suspects they have it) but hasn’t yet found the tools or confidence to dig deeper and uncover what’s really going on.

Here’s what we’ll cover:

• What exactly are IBS-C and Functional Constipation?

• Why these definitions fall short

• The difference between symptoms and root causes

• The top 3 hidden root causes of chronic constipation

• How to start identifying your root cause

Defining IBS-C and Functional Constipation

Let’s start with the basics. According to the Rome III diagnostic criteria, these are the definitions used by most healthcare providers:

IBS-C (Constipation-Dominant IBS) Symptoms include:

• Recurrent abdominal pain or discomfort at least 3 days/month

• Pain improves with bowel movements

• Pain starts when bowel movements become less frequent or harder

• Hard or lumpy stools (Bristol Stool Types 1–2) at least 25% of the time

Functional Constipation Diagnosed when two or more of the following occur:

• Straining during at least 25% of bowel movements

• Hard or lumpy stools for at least 25% of bowel movements

• Sensation of incomplete evacuation or blockage

• Needing manual assistance to pass stool

• Fewer than 3 bowel movements per week

• Loose stools rarely happen without laxatives

• Criteria for IBS are not met

So… What’s the Problem with These Definitions?

Aside from being confusingly similar, the main issue is this: they treat constipation like a condition, when it’s actually a symptom.

By labeling it as a diagnosis, we stop asking why it's happening. This can lead people to believe that irregular bowel movements are just something they have to live with. I’ve even heard medical professionals tell patients that it’s “normal” to not go every day. Spoiler alert: it’s not.

Symptom vs. Root Cause

Think of constipation like a warning light on your car. It’s telling you something’s wrong—but it’s not the actual problem.

• Symptom = what you're feeling (constipation)

• Root cause = why it's happening

You can treat the symptom with a laxative, and that might help short term. But until you find and treat the root cause, the problem isn’t going away—and might even get worse.

The Top 3 Hidden Root Causes of Chronic Constipation

Here are the most common hidden causes of constipation that I see in my clinic. Spoiler: your doctor might not be looking for these.

1. Small Intestinal Bacterial Overgrowth (SIBO)

SIBO is when bacteria that normally live in your large intestine start growing in your small intestine. The wrong types of bacteria (or archaea, which aren’t technically bacteria) ferment carbohydrates and produce gas.

• Hydrogen gas is linked to diarrhea-type SIBO.

• Methane gas, often produced by archaea, slows down gut motility and causes constipation.

If you feel bloated and backed up after meals—this might be the root of your issue.

2. Gut-Brain Axis Dysfunction

Your gut and brain are constantly communicating through the enteric nervous system (your “second brain”). Stress, anxiety, and trauma can seriously disrupt that connection and slow digestion.

When stress becomes chronic and unmanaged, it can reduce gut motility and lead straight to constipation. (So yes—your nervous system plays a massive role in how often you poop.)

3. Gut Microbiome Imbalances (Dysbiosis)

Not all bacteria are bad—but when the balance is off, things go sideways. People with constipation often have too many methane-producing microbes, even in the large intestine.

Unlike SIBO, these microbes belong in the colon, but they've overgrown due to a lack of diversity or overuse of restrictive diets. This overgrowth slows everything down.

So, How Do You Find Your Root Cause?

Here’s how I help clients pinpoint what’s really going on:

• Start with testing. I regularly use SIBO breath tests, and more often than not, we find elevated methane levels. That’s a huge clue and gives us a clear path forward.

• Dig into your history. When did your constipation begin? Were there any big events—like food poisoning, antibiotics, travel, stress, or surgery? We also look at your current diet, lifestyle, sleep, stress levels, and movement. All of these can make or break your gut function.

Often, constipation begins after a root cause is triggered (e.g., SIBO from food poisoning, or slowed motility from anxiety), and then well-meaning changes—like restricting food or under-eating—accidentally make things worse.

Final Thoughts

If you struggle with constipation, know this: there’s always a reason for it.

Daily, complete, and well-formed bowel movements aren’t a luxury—they’re a sign of a healthy gut. You don’t have to settle for “managing” constipation forever. With the right support and information, you can uncover your root cause and get things moving naturally—without long-term dependence on laxatives.