Constipation seems to be very common; we’re frequently asked about it. Constipation can afflict low-carb dieters: It was widely reported among Atkins dieters, and is the most common side effect reported on clinical ketogenic diets for epilepsy. 
Fortunately constipation is usually easily cured. There are a few common causes, and most of them have simple fixes.
Among the most common causes of constipation among low-carbers is deficient antioxidant capacity.
The gut is a challenging environment, full of oxidizing compounds. If glutathione and other antioxidants become deficient in intestinal cells, then the gut becomes leaky , leading to inflammation and the potential for constipation. Oxidative stress can also lead to loss of neurons or neuronal axons from the colon and consequently a loss of motility. Constipation is a common symptom of irritable bowel syndrome.
The cure is simple: supplement. Specifically:
- Selenium, 200 mcg/day (perhaps 400 mcg during a starting period). Selenium is needed for glutathione peroxidase, a glutathione recycling enzyme.
- Vitamin C, 1 g/day (perhaps 4 g/day during a starting period). Vitamin C and glutathione recycle one another.
- Zinc and copper. Total zinc intake should be 30-50 mg/day including food and multivitamin; copper intake should be 2-5 mg/day. Food typically provides 15 mg zinc and 1 mg copper.
- Cysteine and glycine. These are the component amino acids for glutathione. For constipation I would suggest eating some beef gelatin for glycine, and taking one 500 mg capsule of N-acetylcysteine per day.
Egg yolks also increase glutathione production , and eating a dozen per week is highly recommended. Lipoic acid may also help. 
Glutamine, a supplement frequently recommended for gut ailments, can also enhance glutathione production . However, I would generally avoid this, because it can promote proliferation of pathogenic bacteria.
Hypothyroidism may be the most common cause of constipation.
A vicious circle often develops: Gut problems lead to autoimmune hypothyroidism, and constipation is only one symptom of the damage hypothyroidism does to the gut. The vicious circle can be broken by treating the hypothyroidism.
- Eliminate wheat, soy, and other autoimmune-promoting or goitrogenic toxins from the diet.
- Supplement with thyroid supporting nutrients like:
- Selenium (as above).
- Magnesium (citrate or chelate) 200 mg/day.
- Zinc and copper (as above).
- Improve circadian rhythm. Circadian rhythm therapies for hypothyroidism were discussed in two posts, Intermittent Fasting as a Therapy for Hypothyroidism (Dec 1, 2010) and Seth Roberts and Circadian Therapy (Mar 22, 2011).
- See your doctor to consider replacing thyroid hormone and investigating related problems. Your doctor can prescribe thyroid hormone and can explore related problems that may contribute to hypothyroidism, such as adrenal fatigue or iron deficiency.
As always, a few cautions about iodine supplementation. Before starting iodine, eliminate wheat from the diet and supplement with selenium, copper, and magnesium. If you have thyroid-related effects from copper supplementation, before proceeding further supplement copper until your thyroid no longer reacts. Start iodine at a low dose, say 500 mcg (0.5 mg) per day. Increase the iodine dose no faster than one doubling per month. When you increase the dose, if you have a reaction to the higher dose, phase it in: say, alternate between 0.5 mg and 1 mg for a week before trying 1 mg/day every day. Go slowly, plan on spending 4 months to reach 3 mg/day, which is a quarter Iodoral tablet. Tablets can be cut into pieces with razor blades and liquid solutions can be diluted; don’t hesitate to reduce doses.
Insufficient Dietary Fat and/or Bile
Not long ago Jamie Scott (That Paleo Guy), a very smart nutritional advisor, discussed his solution for constipation. There were several gems in there, for instance, that foods that stimulate opioid receptors can cause constipation [5b]:
For example, both gluten grains (and I suspect grains in general) plus dairy contain opiate-like compounds that serve to reduce the motility (movement) of your gut. This effect is commonly seen in those who have to take the likes of codeine (also an opiate) for any length of time.
Chocolate also has opioid peptides. But don’t worry, chocolate isn’t usually the cause of constipation!
But Jamie’s main advice was:
[M]any of the people I work with just are not eating enough fat….
People are a bit skeptical when I suggest increasing fat intake to overcome constipation. Thankfully I can now point to a clinical study in which a high fat diet, in very short time, increased gastrointestinal transit time, reducing the likelihood of constipation occurring;
High-fat diets promote stool passage for several reasons.
- Just a tiny bit of undigested fat can help grease the passage of stool through the colon. Even modest amounts of fat in the stool make it difficult to retain feces and cause fecal incontinence. This is why indigestible oils, like jojoba oil or Olestra, cause diarrhea.
- A second factor is that bile is released into the intestine when fats are eaten, and bile acids have a laxative effect. Both the primary bile acid chenodeoxycholic acid (CDCA) and the secondary bile acid deoxycholic acid (DCA) act as laxatives by inducing water secretion in the colon. An excess of bile therefore causes diarrhea and an insufficiency can cause constipation.  This is why people who have had their gallbladders removed typically develop diarrhea: bile is constantly leaking into the digestive tract.
Just be sure that the high fat you eat comes from healthy natural sources, not high-omega-6 industrially processed seed oils.
Also, bile acid metabolism has a diurnal rhythm.  Improved bile acid metabolism may be another pathway by which circadian rhythm therapies could help constipation.
Insufficient Gut Flora
Fiber is often recommended for constipation, and though I believe insufficient fiber is rarely the primary factor in constipation, it can help by several mechanisms.
First, bacteria, dead and alive, form a large fraction of the stool, and the more fiber you eat, the more bacteria you will have. Bacteria are surrounded by fatty cell membranes which are a little bit slippery.
Second, and probably more important, gut bacteria tend to increase the laxative effect of bile.
This is because the body controls water secretion in the colon in part by sulfation of bile acids; sulfation eliminates the induction of water secretion.
Gut bacteria usually want more water in the colon than the body does, so they’ve evolved sulfatase enzymes that desulfate human bile acids. [8, 9] The desulfated bile causes water release and the stool becomes soft and loose.
Some bacterial species do this more than others – especially virulent strains that spread by inducing diarrhea – and I’m sure everyone’s experienced at some time in their lives what happens when one of these species overpopulates the gut. We often call this “food poisoning” and it can be treated by large doses of probiotics, to displace the bad species with bacteria that release fewer sulfatase enzymes.
At the opposite extreme, if gut bacteria are lacking then bile acids will be excessively sulfated and won’t induce water secretion. Constipation may develop.
Thus, antibiotics can induce constipation. Presumably a zero-carb, zero-fiber diet would also make constipation more likely.
Adding some fiber to your high-fat diet, therefore, can relieve constipation.
Even though choline deficiency is not a proven cause of constipation, I’ll put this in because choline is so important for health. Choline is needed to produce the neurotransmitter acetylcholine. A deficiency of acetylcholine is associated with loss of colonic motility and constipation. 
Egg yolks and liver are good sources of choline. There’s nothing wrong with choline supplementation either.
Some people over-do vitamin D supplementation and/or calcium supplementation. Elevated blood calcium levels, which can be brought about by too much vitamin D, will cause constipation. If you supplement either vitamin D or calcium and have constipation, ask your doctor to check serum 25OHD, 1,25D, and calcium levels.
Some pathogenic bacteria are able to paralyze the gut and induce constipation. Some bacterial species that induce diarrhea can also induce constipation when they choose – for instance, C. difficile. This is one reason why patients with bowel disorders such as Irritable Bowel Syndrome or ulcerative colitis often experience both constipation and diarrhea.
Antibiotics like vancomycin that work well against Clostridium have successfully reversed cases of constipation. 
Infection-induced constipation may also cause bloating, gas, acid reflux, and gastroparesis, so if your constipation is accompanied by these symptoms you should see a doctor.
Don’t over-use laxatives
It can be risky to over-use laxatives. The riskiest is probably senna, which promotes bowel movements by (a) inhibiting water absorption by the colon and (b) promoting muscle spasms in the colon wall. Unfortunately, senna is a toxin that can cause lasting damage, notably to nerves.
If you must use laxatives, magnesium citrate liquids are the best. This will restore your body’s magnesium status as well as promote clearing of the bowels.
With good diet and nutrition, and normalization of thyroid function, constipation is usually easily cured. The exceptional cases are those of chronic gut infections; these may require some detective work on the part of a doctor.
I’m sure this reads like a laundry list, but it should give those with constipation some ideas!
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