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TMI warning: how fish oil did not work for me

When I was in my late twenties, I started taking fish oil supplements for the first time. I tolerated them well and they, in conjunction with my other supplements and lifestyle changes, led to an amazingly healthy period for me—I actually went weeks without a migraine.

As I do, I fell off the wagon and climbed back on. I’ve done this many times over the years, but I didn’t reincorporate fish oil again until about six months ago when my neurologist was displeased with my migraine improvement (or lack thereof) and wanted me to add an extra dose of magnesium as well as daily omega-3 and omega-6 fatty acids, in the form of fish oil capsules.

(If you don’t want to read more about poo, it’s probably time for you to dip out—we’re definitely entering #TMI land.)

I started noticing something weird about my once- or twice-daily trips to the bathroom: my poop smelled like my cat’s poop. A putrid, acrid smell. What in the world?

I stuck with the fish oil capsules even after that, not quite sure what was up. My alarmist, hypochondriac side thought, I guess Satchel and I have the same deadly illness that makes our poop smell so awful. Luckily that side doesn’t usually have a very loud voice, and it shuts up quickly.

A few days later, I opened a can of wet food for the cat and tried to avoid breathing in the smell of what the pet food company calls “Seafood Deluxe Dinner.” But I couldn’t help but catch a whiff. That smell was…familiar. That smell made me think of my bathroom, where not only I but my cat use the restroom (he in a litter box, mind you—we aren’t clever enough to have toilet-trained him).

OMG, I thought. Duh. Satchel started eating canned food with a ton of fish in it right when I started taking daily fish oil. That’s why we both have this awful-smelling #2! (Luckily he was spared the diarrhea.)

I had bought the same brand I’d used before with no problems, so didn’t even consider that the fish oil was the reason behind my GI issues.

The longer I stuck with the twice-daily capsules I realized I hadn’t changed much else in my life or diet since adding them in. I decided to use freshly ground flaxseed (a great source for omega-3) in my then-daily smoothies instead of the fish oil capusles, and the problem went away.

Later, at my appointment, my neurologist seemed quite surprised to hear that the fish oil was making me have diarrhea or soft stools most of the time—apparently she doesn’t have other patients who’ve had that same issue. She told me the flaxseed was fine for now as long as I made sure to grind it fresh and keep it refrigerated (which I do).

Have you ever had a weird side effect from fish oil capsules? Along those lines, are their any drugs or treatments you’ve tried that gave you weird symptoms that the doctor didn’t recognize? 

This article represents the opinions, thoughts, and experiences of the author; none of this content has been paid for by any advertiser. The team does not recommend or endorse any products or treatments discussed herein. Learn more about how we maintain editorial integrity here.


  • Victoria
    3 years ago

    I take vegetarian Omega 3 supplements that are sourced from algae instead of fish. No fish burps or upset stomach, and no gelatin (which is a migraine trigger for me). Whole Health on the Internet carries it.

  • Victry
    3 years ago

    Feverfew gave me nightmares. Terrible, horrible, realistic, nightmares. I wasn’t sure what was worse, the hell when I slept or the hell (migraine) when I was awake.

  • Liz Flynn
    3 years ago

    I can not vouch for the math but I’ve read that eating 3 or 4 cans of sardines a week will eliminate the need for fish oil supplements. Sardines are packed with other nutrients as well. Now, 3 or 4 cans per week would be a lot of sardines for me even though I do enjoy sardines. It is a healthy option worth considering though (or maybe a mix of sardines & other foods rich in omega-3’s). Just think how jealous the cat would be!

  • Eleanor R.
    3 years ago

    Why do you think it was the fish oil? You increased your dose of magnesium at the same time. I tried a migraine dose of Mg for several months a few years ago, and eventually got soft stools and had to stop taking it. I still don’t tolerate Mg (and I had done enough research to only take the “good” kind.) Some times I can tolerate 70 mg. Magnesium Malate; right now not even that.

  • wendy
    3 years ago

    I’ve heard some magnesium supplements, especially if you are taking arginine powder (you mix it with water) can cause loose stools, if taken too much, so maybe it was the combo. Regardless, glad you are doing better.

  • Luna
    3 years ago

    Years ago I was taking a coQ10 with fish oil softgel. Not much fish oil in it but the fish oil burp a while later was unpleasant so I finally stopped. Used to take flax oil regularly then stopped. A few years later was advised to take it again instead of the ground flax seed. It tasted awful!!! Was so irritated because it wasn’t cheap. Boswellia gives me strange side effects no one else heard of. Life is interesting.

  • Liz Flynn
    3 years ago

    Luna I also get unusual side effects – to many OTC meds, as well as supplements and herbs with innocuous reputations. I’ve never tried Boswellia but I do get the fish oil burp with a heartburn bonus. Life is interesting! Take good care.

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