Fecal Transplant At Home – DIY Instructions

fecal transplant at home




These “Fecal Transplant At Home – DIY Instructions” are based on the experiences of one person, the anecdotal reports of others and questions most frequently asked by  e-Patients. They are not medical advice. Please read the disclaimer and discuss your options with your doctor before doing fecal microbiota transplant (FMT). It is critical that your doctor test your donor before FMT. An outwardly healthy person could carry an asymptomatic parasite or blood borne illness that could wreak havoc in your fragile system.


These instructions are for fecal transplant at home using an enema bag or bucket hung on a wall, which will maximise flow up the colon from the force of gravity. If you are in a hurry, syringes and enema bottles can also be used but do try to use the enema bag method as often as possible, for maximum effect. These are solo DIY instructions and do not require assistance from another person.


Shopping List 

fecal transplant shopping list


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Before the Big Day 

  • Find and test your donor. Opinions differ about the minimum testing required. See here for testing options.
  • Read the CDD Home Infusion Protocol for Donor & Recipient
  • Read every Frequently Asked Question on this site. Don’t be lazy about this. You are putting someone’s poop up you.  To make an informed decision you must research the possible risks as well as the possible benefits.
  • Familiarise yourself with the Bristol Stool Chart so you know what healthy poop looks like (2,3, 4 on this chart).
  • Familiarise yourself with the shape and position of your colon so that you understand the direction in which the FMT will flow.

    biofilm busters disrupt colonies of pathogenic microbiota, weakening their resistance

  • Decide if you are going to use anti-biotics / herbal anti-microbials / biofilm busters etc to kill off bad bugs before FMT. This is not mandatory, opinions differ.
  • Decide if you are going to do a bowel-washout (lavage) or not. This is not mandatory, opinions differ. The goal of a washout is to minimise the amount of old poop present at the time of infusion of the new poop. Fasting or low-fibre liquid diets help achieve this.
  • If you have IBD take whatever medication you know will control the inflammation. Do not do FMT in a flare unless you have no choice.
  • Decide where you will do your FMT – either in a bath or lying on a towel on the bathroom floor. Avoid doing it on a bed or sofa or in a carpeted area in case you have a spill.
  • Purchase supplies.
  • Hang a heavy duty adhesive hook on the wall at a height that will allow for the tube to reach your body without too much slack. Too high and the tube will not reach. Too low and you won’t get enough flow from gravity.
  • Decide if you are going to use distilled water or saline. Opinions differ which is better so you may have to experiment. Some have reported that saline has a laxative effect. Others have reported that saline is easier to hold in.
  • Do a practice run with your enema bag using just distilled water.
  • Go on a low fibre diet for 2 weeks prior to FMT.
  • If this is the first in a series of FMTs you can clear out the contents of your bowel 24 hours prior to FMT by fasting and using a laxative or water diet beforehand DO NOT DO THIS EVERY TIME AS IT WILL DISRUPT GROWTH OF THE NEW FLORA. This step is optional.
  • Stop anti-biotics/anti-microbials etc 24 hours before FMT (48 hours if you have not done a bowel wash-out – longer if constipated).
  • Take medications as usual.
  • Leave plastic food containers or zip lock bags with your donor for collection of sample
  • If weather is cold leave a microwavable heat pack with your donor so that it can gently keep the sample as close to body temperature as possible while waiting to be collected.

On the Big Day

  • fecal transplant at homePrepare your FMT area. Put enema bag, lubricant, tissues, paper towels, plastic bag, diagram of colon & timer within easy reach together with anything you need to be comfortable eg rug and pillow. The cushion should go underneath the towel so that it raises your rear end. This will use gravity to keep the FMT in.  
  • Assume you will have a spill and make sure paper towels and plastic bag are nearby to dispose of clean-up items. A bath is easier as you can wash the mess away.
  • Take Imodium upon waking (unless you suffer constipation).
  • Collect sample.
  • Do not use sample if it does not look healthy. Sample should look like 2, 3 or 4 on the Bristol Stool Chart.
  • Keep sample at room temperature and use within 2-3 hours unless freezing.
  • If you are going to freeze some sample, separate it into portions and put it in the freezer.
  • Heat distilled water in microwave so that it is tepid (the temperature of a baby’s bottle). Too hot will kill the FMT and too cold will be uncomfortable for you to hold in.
  • To make saline add ¼ tsp. sea salt to 1 cup distilled water. Do not use table salt with additives.
  • Put sample in blender or zip lock bag and lightly mush/blend with water. If blending don’t overdo it as too much air will reduce the potency of the sample. Zip-lock bags require less clean up than blender-method and expose the microbiota to less turbulence, but the process is somewhat more revolting as you are closer to the poop and have to mush it by hand through the bag. Your choice.
  • Add as much water as necessary to make the FMT the consistency of paint. Too thick will block the nozzle and too runny will be harder to hold in and reduce the potency of the FMT.
  • Take care not to expose the sample to any more air or water than absolutely necessary as this will reduce its quality.
  • Make sure enema nozzle switch is shut. VERY important or it will spurt everywhere!
  • Pour FMT slurry into enema bag using kitchen strainer & funnel
  • Hang enema bag on hook.
  • Lift tube high in the air (to prevent spill), release nozzle to let air out, lower gradually until all air is released. Close nozzle once you can see all air has gone and FMT has reached the nozzle.
  • CSS-10011-3

    use sea salt without additives to make saline and disinfect your FMT equipment

    Prepare for entry with a little lubricant

  • Lie down on your left side making sure your rear is raised on the cushion.
  • Lift up your right leg and slowly, gently insert enem
    a nozzle. A little discomfort is normal but do not continue if it is painful. It can help to dilate the entry with a finger before insertion.
  • Open the enema nozzle switch.
  • Feel the FMT flowing. If it’s not flowing sit up, carefully holding the nozzle in place and shake the enema bag to get it flowing.
  • Lie down and take a deep breath as the FMT flows in. Hold your butt tight. Congratulate yourself for having got this far. Think of all the good bugs that are going to repopulate your gut. Breathe.
  • If you feel like you are going to expel the FMT then turn off the enema nozzle. You can put more in later.
  • Refresh your memory by looking at the diagram of the colon.
  • Lie on your left side for 10 minutes. Massage the FMT gently up your colon.
  • Switch off the enema nozzle, then remove the nozzle and put it straight into the plastic bag. Wipe yourself if necessary.
  • Lie on your stomach for 10 minutes.
  • Lie on your back for 10 minutes. Massage the FMT gently across your colon.
  • Lie on your right side for 10 minutes. Massage the FMT gently down your colon.
  • If you are having trouble holding it in, don’t panic. It doesn’t matter if you lose a little. That’s what the big brown towel and paper towels are for. Try doing a little at a time, massaging, and then doing some more.
  • Try and hold it in for at least 6 hours.
  • If you are using a re-useable enema bag, wash it and store it in a bucket of water with 1 lb. / 500g of dissolved sea salt.

After the Big Day 

  • You will get into a routine with FMT. The first time is the hardest and like everything it gets easier with practice. Hopefully you won’t have to do it for too long.
  • Only continue the Imodium if you are having trouble holding in the FMT.
  • If you suffer from food intolerances and react to the donor’s food, use less FMT or ask your donor to modify their diet. A little used frequently is better than a lot used occasionally.
  • A high fiber diet will help grow your new microbiota, but don’t overdo it. Not all fibers agree with all people. Experiment until you find the right ones. Only take a fiber supplement if you cannot get enough fiber through your diet. If you have IBD you will need to go easy on the fiber until your gut wall can cope, and then introduce it only slowly.   
  • If you have food intolerances don’t try anything that isn’t a known safe food (or supplement), for at least 3 months after FMT and then only introduce slowly.
  • If you experience die-off or side effects, try a liver tonic to support your liver which may be under pressure from the readjustment occurring in your gut. 
  • .If you suffer from intestinal permeability (leaky gut) try one of the repair formulas available. It might take a few to find one that has the right mix of ingredients for you. Perm-a-Vit and Intestinew have a good mix of gut healing ingredients. Customised formulas are also available from some naturopathic practitioners.
  • Get your zinc levels tested and make sure they are on the high side of normal. ZInc is essential for healing. Zinc Lozenges are better than tablets as they bypass the digestive system.
  • If you have IBD read the Briggs Protocol which contains a step by step gut repair strategy
  • If FMT doesn’t work for you, try a different donor or investigate factors that might be disrupting growth of the new flora.

feed your new microbiota fiber

leaky gut repair formula

repair your gut wall


help your liver deal with die-off and gut toxins

 enhanced zinc

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Frozen FMT Instructions 

Frozen FMT allows you the flexibility that a donor doesn’t. But it is reported not to have the same ‘hit’ as fresh as the quality is compromised by freezing in home refrigerators.

There are three ways to freeze FMT. When you do a fresh FMT you can pour some of the slurry into ice cubes and keep them to use as needed. Add a few drops of liquid glycerol to preserve it, not too much as it is a laxative.  

However to maximise the potency of the FMT it is best to freeze the sample without adding water. The more interference (air and water) the more the potency is compromised. To do this, you distribute the sample into ice cubes or cupcake trays. Alternately freeze it whole and break it up later by putting it into two plastic bags and hitting it with a hammer.

The amount of frozen FMT you use will depend on how much you have and when you will next see your donor. There are no hard and fast rules. Considering that pro-biotics come in tiny capsules you really don’t need much FMT to make a difference, especially if you are doing it regularly.

To defrost FMT put it in a cup of warm distilled water/saline and keep stirring until it’s dissolved. If you find this too revolting then put it in the blender. The water should be warm enough so that the end mix will be tepid, a comfortable temperature to have inside you, but not so hot that the good bacteria are killed. If the mix is too cold once defrosted, simply add a little warm water. Once it’s defrosted strain the mix into an enema bag as per above instructions. Where possible, always do FMT when your bowel has been emptied.

We don’t yet know how long frozen stool can be kept. One person has used it after 10 months without adverse affects. OpenBiome states that although further research has yet to be done “microbiological culturing experience suggests that samples may be stored for up to 6 months at -20°C without a significant loss of viability”.


How to Make Microbiota Capsules


Discussion Forums 

Facebook Fecal Microbiota Transplant

Facebook Bacteriotherapy

Getting Healthier Now – FMT

Yahoo FMT for Crohns & Colitis


Other Resources 


Where to Start – a To Do List

Is Fecal Transplant for You?

How to Find a Donor



Kathy’s YouTube video on how to do enema bottle method

Michael’s YouTube video on how to do enema bottle method


You are welcome to reproduce the above instructions provided you don’t make any changes and provide a link to the PoP website.



These instructions are based on the experiences of one person, the anecdotal reports of others and questions most frequently asked by e-Patients. They are not medical advice. Please read the disclaimer and discuss your options with your doctor before doing FMT. It is critical that your doctor test your donor before FMT. An outwardly healthy person could be carrying an asymptomatic parasite or blood borne illness that could wreak havoc in your fragile system.



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