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Carbohydrate Intolerance: It’s Not What You Think It Is

Do You Have Carbohydrate Intolerance or Carbohydrate Malabsorption?

Key Takeaways
  • If you experience bloating, diarrhea, or nausea after eating carbohydrates, you may have carbohydrate maldigestion (sometimes less accurately referred to as carbohydrate intolerance).
  • Carbohydrate maldigestion is when the body is lacking enzymes to digest carbohydrates, a common example being lactose intolerance.
  • Carbohydrate malabsorption is an inability of carbohydrates to move across the intestinal wall into the bloodstream to be used by the body, a few common examples being SIBO and leaky gut.
  • A low FODMAP diet can help improve both carbohydrate malabsorption and maldigestion.
  • In popular health blogs the term carbohydrate tolerance may be used to refer to glucose regulation, but is unrelated to the ability to digest or absorb carbohydrates.
  • You can improve your glucose regulation with a lower carbohydrate diet, exercise, and sleep.

Do you get brain fog, bloating, nausea, stool changes, or fatigue soon after eating a high-carb meal? You may be dealing with “carbohydrate intolerance,” more accurately referred to as carbohydrate maldigestion — the inability to digest carbs. 

While carbohydrate maldigestion specifically refers to a lack of enzymes needed to digest carbs in the digestive tract, it’s closely related to (and sometimes the cause of) carbohydrate malabsorption. Carbohydrate malabsorption occurs when carbohydrates cannot be absorbed in the gut in order to be utilized by the body. Both carbohydrate maldigestion and malabsorption can result from a variety of different causes, with a primary example being small intestinal bacterial overgrowth (SIBO). 

This article will help you understand what carbohydrate intolerance, maldigestion, and malabsorption really mean and how they differ from the popularized term carbohydrate tolerance (which deals with blood sugar regulation). Even more, we’ll help you navigate any issues you have with digesting and metabolizing carbohydrates. 

What Is Carbohydrate Intolerance Really?

There are a few differences between carbohydrate intolerance, carbohydrate malabsorption, and carbohydrate maldigestion — and while it might seem like the terminology doesn’t matter, understanding which issue is behind your symptoms can help you determine how to address it. 

Traditionally speaking, carbohydrate intolerance refers to an inability to digest carbohydrates or the fermentation of carbohydrates in the gut. The Merck Manual defines it as “the inability to digest certain carbohydrates due to a lack of one or more intestinal enzymes.” 

One common example of this is the specific condition known as lactose intolerance, or a difficulty with digesting dairy, which is characterized by the absence of an important digestive enzyme known as lactase. However, this conventional definition of carbohydrate intolerance has evolved over time and been renamed “carbohydrate maldigestion.” 

Today, many healthcare practitioners have adopted the term “carbohydrate tolerance” to refer to the body’s general ability to metabolize carbs (similar to the concept of glucose regulation). However, this is not to be confused with carbohydrate intolerance, which is simply a vague and outdated term for a difficulty with digesting carbohydrates. 

To maintain clarity and follow updated practices for this article, we’ll use more medically accurate definitions for the terms carbohydrate tolerance, carbohydrate malabsorption, and carbohydrate maldigestion. 

TermSummary DefinitionCommon Causes
Carbohydrate tolerance A non-medical term to describe each person’s unique metabolic and digestive responses to carbs in the diet [1]. It borrows from the medical condition of glucose intolerance, which leads to issues with insulin regulation [1].If a person has issues with carbohydrate tolerance, they have poor glucose tolerance that may result in diabetes or insulin resistance [2].
Carbohydrate malabsorptionThe inability of carbohydrates to be absorbed (move across the intestinal wall into the bloodstream) for use by tissues and organs [3].Could be a result of carbohydrate maldigestion/enzyme deficiencies described above.

Another cause of carb malabsorption is damage to the intestinal mucosa from intestinal diseases (celiac disease, Crohn’s disease, SIBO), gastrointestinal surgery, drug toxins (such as antibiotics), or radiation, all of which can prevent simple sugars from crossing the intestinal wall [3, 4].
Carbohydrate maldigestionA genetic or acquired deficiency of enzymes that break down carbs into simple sugars that are small enough to be absorbed in the GI tract (Merck Manual). May be a result of a congenital or acquired carbohydrate maldigestion such as disaccharidase deficiencies or a sodium-dependent glucose transporter-1 deficiency [3, 4].

The most common form is lactose maldigestion (often called lactose intolerance), where the lactase enzyme needed to digest the lactose carbohydrate in dairy products isn’t present.

We’ll refer to “carbohydrate maldigestion” for the medically recognized condition related to enzyme deficiencies, “carbohydrate malabsorption” in reference to the general inability of the GI tract to absorb carbohydrates for use by the body either from genetics or due to damage of the gut lining, and “carbohydrate tolerance” to refer to glucose tolerance.

So, if there’s so much confusion over these terms, how do you know what you might be dealing with?

If you are having non-specific symptoms such as brain fog, headaches, fatigue, or hyperglycemia after eating carbs, it’s more likely that you have a problem with carbohydrate tolerance and are struggling with glucose regulation.

If you’re having symptoms of fatigue and brain fog with additional gastrointestinal symptoms such as bloating, abdominal cramps, or diarrhea, then you may be dealing with carbohydrate maldigestion or malabsorption. 

Since you’re likely looking for answers related to a difficulty with digesting carbohydrates (and not those related to blood sugar imbalances), let’s dive into carbohydrate maldigestion and malabsorption first.

Carbohydrate Malabsorption and Carbohydrate Maldigestion

Carbohydrate malabsorption and maldigestion are often discussed together because many of the symptoms are similar and one can lead into the other. 

As we defined earlier, carbohydrate maldigestion is when carbohydrates aren’t able to be digested properly, most often from a lack of certain digestive enzymes. Whereas malabsorption is the inability of carbohydrates to move across the intestinal wall into the bloodstream for use by tissues and organs. 

A person with maldigestion may also have carbohydrate malabsorption from a lack of the enzymes needed to break down carbohydrates, which results in carbohydrates not being able to move across the intestinal wall to the bloodstream. 

The symptoms of both of these are often similar, including (Merck Manual):

  • Diarrhea
  • Bloating
  • Excessive gas and flatulence
  • Nausea
  • Gut burbles/rumbles/gurgles
  • Abdominal pain and cramping

You may notice that these symptoms are also similar to those of IBS (irritable bowel syndrome), colitis, and Crohn’s disease. Because these gastrointestinal disorders affect the lining of the gut, they can also lead to carbohydrate malabsorption. 

Carbohydrate Maldigestion and SIBO

SIBO, small intestinal bacterial overgrowth, occurs when there’s an overgrowth of bacteria in the small intestine. This dysbiosis can destroy the villi (tiny structures made up of cells) lining the gut and impair the production of enzymes (disaccharidases) needed to digest carbohydrates, making it a potential culprit of carbohydrate maldigestion [3].

These undigested carbohydrates are then fermented by excess bacteria in the gut, which is why people with SIBO may have symptoms such as bloating, rumbling in the stomach, and gas.

At the Ruscio Institute for Functional Health, if a patient experiences fatigue and/or nausea 30 to 90 minutes after a high-carb meal, we suspect some form of gut dysbiosis or SIBO, in which bacterial fermentation of carbohydrates is causing GI symptoms as well as fatigue or brain fog

Observational studies and literature reviews explain that carbohydrate maldigestion and SIBO can both lead to carbohydrate malabsorption by impairing the absorption of monosaccharides (simple sugars such as glucose, fructose, and galactose) from the gut into the bloodstream for use throughout the body [5].

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Whether or not SIBO is the cause of an existing carbohydrate maldigestion, we know that both can occur in one person at the same time, making it difficult to diagnose one or the other, or both [6, 7].

There’s also a link between SIBO and lactose intolerance, a form of carbohydrate maldigestion. A 2017 observational study found that 81% of SIBO-positive patients were also positive for lactose when given a hydrogen-positive lactulose breath test [7].

Another study found that in patients with suspected carb maldigestion [8]:

  • 78 (25.5%) of the patients had genetic primary lactose maldigestion 
  • 34 (11.1%) had fructose maldigestion
  • 57 (18.6%) had sorbitol maldigestion
  • 29 (9.5%) with early peaks in hydrogen or methane on breath tests had SIBO

If you’re found to have both SIBO and carbohydrate maldigestion, you should change your diet to avoid the effects of undigested sugars (carbohydrates) and consider treating SIBO with prescription antibiotics or herbal antimicrobials [8].

If you continue to have gastrointestinal symptoms when eating carbohydrates, even after treating SIBO, it’s likely that you have another factor that is contributing to your carbohydrate maldigestion. 

For example, if you have inherited lactose intolerance you would avoid dairy products because they contain the sugar (carbohydrate) lactose. You may also have acquired carbohydrate maldigestion if a condition has damaged the intestinal lining, such as in celiac disease, and you may need to avoid foods that contain gluten (wheat) (Merck Manual).

Some research has also found that probiotics can help to improve lactose tolerance [9, 10].

In order of operations, if you’re found to have SIBO, treat the SIBO first to see how much you improve. If your symptoms don’t completely resolve after the SIBO is cleared, then another cause of carbohydrate maldigestion or malabsorption may be present, and you would need to avoid consumption of indigestible carbohydrates (Merck Manual).

What About FODMAPs?

FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. These are types of carbohydrates that, when fermented by gut bacteria (such as in the case of carbohydrate maldigestion and malabsorption), can cause the large intestine to expand and create symptoms like bloating and diarrhea [11]. These carbohydrates are found in most milk products, legumes, most whole grains, certain vegetables, fruits, and many sweeteners.

The best way to improve these symptoms is to go on a low FODMAP diet [11].

If you’re found to have SIBO, your healthcare professional may also put you on a low FODMAP diet because restricting bacteria-feeding carbs has been shown to improve SIBO and even IBS symptoms [12, 13, 14, 15].

What this research on carbohydrate maldigestion and malabsorption shows us is that issues with how the body processes and uses carbohydrates are vast and sometimes complex. Any one person can have multiple reasons why their body isn’t digesting or absorbing carbohydrates properly.

The good news is that the interventions that help with most underlying causes of carbohydrate malabsorption or maldigestion are similar.

A low FODMAP diet not only removes types of carbohydrates that ferment in the gut for some people, but these same foods often are the carbohydrates that the bacteria that cause SIBO proliferate on. A low FODMAP diet also removes many of the carbohydrates that people may not be able to digest, such as dairy products that contain lactose and fructose for people who have fructose malabsorption or fructose intolerance. 

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Carbohydrate Tolerance and Glucose Regulation

Carbohydrate tolerance isn’t a medically recognized term, but is commonly used to refer to the function of how well our body responds to carbohydrates. If we have a poor metabolic response to carbohydrates, our blood sugar levels are often erratic, frequently seen on a blood glucose monitor, and we may feel tired, “hangry,” and confused. It’s loosely based on the medically recognized condition of glucose intolerance and insulin resistance. 

Glucose intolerance refers to the abnormal blood sugar levels that can lead to pre-diabetes, diabetes mellitus, or gestational diabetes [2].

Insulin resistance refers to the body’s blunted response to insulin (the hormone that lowers blood glucose), due to chronically elevated blood sugar levels. That high glucose in the blood is what can later lead to type 2 diabetes [16]. It occurs in about 24% of U.S. adults and starts about 10 to 15 years before developing type 2 diabetes.

Symptoms of insulin resistance may include [16, 17]:

  • Weakness and fatigue
  • Brain fog
  • Excessive need to pee and excessive thirst
  • Blurry vision 
  • Skin tags
  • Rapid heart beat after higher-carb meals
  • Intense craving for carbohydrates (feeling compelled to eat sweets)
  • Feeling hangry (hungry and angry) sooner than four hours between meals

When people talk about improving your carbohydrate tolerance, what they’re often referring to is improving glucose regulation in your body so you don’t develop insulin resistance, but also so you can have more energy, better focus, and better mood regulation.

The best treatment for poor glucose regulation and preventing or improving insulin resistance is to lower your carbohydrate intake, get adequate sleep to help regulate hormones, and to exercise regularly to increase muscular insulin sensitivity [1, 18].

Managing Your Carbohydrates for Better Health

If you find that you’re struggling with symptoms such as brain fog, fatigue, carb cravings, and being hangry shortly after meals, you may mainly be dealing with poor glucose regulation. In that case, a Paleo low-carb diet, good sleep, and exercise are a great place to start. 

However, if you have the above cognitive and performance symptoms, plus gastrointestinal symptoms, you may be dealing with some form of carbohydrate malabsorption or maldigestion. 

Trying a low FODMAP diet is a great first step that may help you get relief from symptoms. Try a low FODMAP diet for a month and record any improvements in your symptoms.

I know how frustrating it can be to struggle with so many symptoms and not know exactly what is causing them. If you’re wondering if you may have SIBO or some other underlying condition causing carbohydrate malabsorption or maldigestion, even after trying dietary and lifestyle interventions, we would be happy to help you at the clinic. Fill out the new patient form to get started on your healing journey.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

➕ References

  1. Carb Tolerance: A Beginner’s Guide | Carb Manager [Internet]. Available from:
  2. Goyal R, Nguyen M, Jialal I. Glucose Intolerance. In: StatPearls. Treasure Island (FL): StatPearls Publishing; 2022. PMID: 29763085.
  3. Omer A, Quigley EMM. Carbohydrate maldigestion and malabsorption. Clin Gastroenterol Hepatol. 2018 Aug;16(8):1197–9. DOI: 10.1016/j.cgh.2018.01.048. PMID: 29425782.
  4. Raithel M, Weidenhiller M, Hagel AF-K, Hetterich U, Neurath MF, Konturek PC. The malabsorption of commonly occurring mono and disaccharides: levels of investigation and differential diagnoses. Dtsch Arztebl Int. 2013 Nov 15;110(46):775–82. DOI: 10.3238/arztebl.2013.0775. PMID: 24300825. PMCID: PMC3855820.
  5. Varjú P, Ystad B, Gede N, Hegyi P, Pécsi D, Czimmer J. The role of small intestinal bacterial overgrowth and false positive diagnosis of lactose intolerance in southwest Hungary-A retrospective observational study. PLoS ONE. 2020 May 8;15(5):e0230784. DOI: 10.1371/journal.pone.0230784. PMID: 32384113. PMCID: PMC7209350.
  6. Perets TT, Hamouda D, Layfer O, Ashorov O, Boltin D, Levy S, et al. Small intestinal bacterial overgrowth may increase the likelihood of lactose and sorbitol but not fructose intolerance false positive diagnosis. Ann Clin Lab Sci. 2017 Aug;47(4):447–51. PMID: 28801371.
  7. Enko D, Kriegshäuser G, Kimbacher C, Stolba R, Mangge H, Halwachs-Baumann G. Carbohydrate Malabsorption and Putative Carbohydrate-Specific Small Intestinal Bacterial Overgrowth: Prevalence and Diagnostic Overlap Observed in an Austrian Outpatient Center. Digestion. 2015 Jun 25;92(1):32–8. DOI: 10.1159/000430981. PMID: 26138365.
  8. Rasinkangas P, Forssten SD, Marttinen M, Ibarra A, Bothe G, Junnila J, et al. Bifidobacterium animalis subsp. lactis Bi-07 supports lactose digestion in vitro and in randomized, placebo- and lactase-controlled clinical trials. Am J Clin Nutr. 2022 Dec 19;116(6):1580–94. DOI: 10.1093/ajcn/nqac264. PMID: 36149331. PMCID: PMC9761758.
  9. Oliveira LS de, Wendt GW, Crestani APJ, Casaril KBPB. The use of probiotics and prebiotics can enable the ingestion of dairy products by lactose intolerant individuals. Clin Nutr. 2022 Dec;41(12):2644–50. DOI: 10.1016/j.clnu.2022.10.003. PMID: 36308983.
  10. Berni Canani R, Pezzella V, Amoroso A, Cozzolino T, Di Scala C, Passariello A. Diagnosing and treating intolerance to carbohydrates in children. Nutrients. 2016 Mar 10;8(3):157. DOI: 10.3390/nu8030157. PMID: 26978392. PMCID: PMC4808885.
  11. Staudacher HM, Whelan K. The low FODMAP diet: recent advances in understanding its mechanisms and efficacy in IBS. Gut. 2017 Aug;66(8):1517–27. DOI: 10.1136/gutjnl-2017-313750. PMID: 28592442.
  12. Marsh A, Eslick EM, Eslick GD. Does a diet low in FODMAPs reduce symptoms associated with functional gastrointestinal disorders? A comprehensive systematic review and meta-analysis. Eur J Nutr. 2016 Apr;55(3):897–906. DOI: 10.1007/s00394-015-0922-1. PMID: 25982757.
  13. Schumann D, Klose P, Lauche R, Dobos G, Langhorst J, Cramer H. Low fermentable, oligo-, di-, mono-saccharides and polyol diet in the treatment of irritable bowel syndrome: A systematic review and meta-analysis. Nutrition. 2018 Jan;45:24–31. DOI: 10.1016/j.nut.2017.07.004. PMID: 29129233.
  14. Altobelli E, Del Negro V, Angeletti PM, Latella G. Low-FODMAP Diet Improves Irritable Bowel Syndrome Symptoms: A Meta-Analysis. Nutrients. 2017 Aug 26;9(9). DOI: 10.3390/nu9090940. PMID: 28846594. PMCID: PMC5622700.
  15. Insulin Resistance: What It Is, Causes, Symptoms & Treatment [Internet]. Available from:
  16. High blood sugar – self-care: MedlinePlus Medical Encyclopedia [Internet]. Available from:
  17. Freeman AM, Pennings N. Insulin Resistance. In: StatPearls. Treasure Island (FL): StatPearls Publishing; 2022. PMID: 29939616.

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