Does Choline Make Urine Smell? Understanding the Fishy Odor Connection

October 19, 2025 •

4 min read

While choline is an essential nutrient vital for liver function, brain development, and nerve signaling, an unpleasant fishy odor can sometimes be a side effect of its consumption. For most people, consuming choline from food or supplements does not cause a noticeable smell, but for others, particularly at high doses or due to an underlying metabolic issue, a distinctive odor can occur. So, does choline make urine smell? It's a complex metabolic process that hinges on gut bacteria and liver enzymes.

Quick Summary

Choline consumption can lead to a fishy urine odor due to the production of trimethylamine (TMA) by gut bacteria. In individuals with the genetic disorder trimethylaminuria (TMAU) or those consuming high choline doses, the liver cannot properly process TMA, causing it to be excreted through sweat, breath, and urine.

Key Points

TMA Production: Gut bacteria break down choline into trimethylamine (TMA), the compound responsible for the fishy odor.
FMO3 Enzyme Failure: In most people, the liver's FMO3 enzyme neutralizes TMA, but a genetic defect (TMAU) or precursor overload can impair this process.
Trimethylaminuria (TMAU): A rare inherited disorder where the FMO3 gene mutation prevents proper TMA metabolism, causing persistent fishy odor in bodily fluids.
High-Dose Supplements: Even without a genetic defect, very high doses of choline or lecithin supplements can overwhelm the FMO3 enzyme, causing a temporary odor.
Management Strategies: Reducing intake of high-choline foods, discontinuing high-dose supplements, using low-pH soaps, and staying hydrated are effective ways to manage the odor.
Professional Guidance: A healthcare provider can diagnose TMAU or other underlying issues and provide specific advice on diet and potential medical treatments.

The Metabolic Pathway from Choline to Odor

To understand why choline can result in a fishy smell, it's crucial to examine its metabolic journey in the body. The process begins in the gut, where bacteria break down choline from various food sources into a compound called trimethylamine, or TMA.

In most healthy individuals, the liver has a functioning enzyme called flavin-containing monooxygenase 3 (FMO3). This enzyme quickly converts the foul-smelling TMA into an odorless compound known as trimethylamine N-oxide (TMAO). The TMAO is then easily excreted by the kidneys through the urine without any detectable odor.

However, problems can arise when this conversion process is disrupted. When the liver's ability to metabolize TMA is impaired or overwhelmed, the smelly TMA accumulates in the body instead of being neutralized. This excess TMA is then released through bodily secretions, including urine, sweat, and breath, producing the characteristic strong, fishy odor.

Trimethylaminuria (TMAU): The Genetic Link

For a small percentage of the population, the fishy odor is not a temporary side effect of a high-choline meal but a persistent condition caused by a genetic disorder called trimethylaminuria (TMAU), or "fish odor syndrome".

Primary TMAU: This form is inherited and results from a mutation in the FMO3 gene. A person must inherit two copies of the mutated gene (one from each parent) to develop the condition, which means their FMO3 enzyme is either missing or non-functional. This metabolic defect prevents the conversion of TMA to TMAO, leading to a consistent body odor.
Secondary TMAU: In some cases, the condition can be acquired later in life due to factors that temporarily inhibit or overwhelm the FMO3 enzyme's function. This can be caused by conditions such as liver failure or certain kidney diseases that interfere with the normal detoxification process.

High Intake and Other Factors

Even without a genetic predisposition to TMAU, consuming excessive amounts of choline can overwhelm the liver's FMO3 enzyme, causing a transient fishy odor. The Tolerable Upper Intake Level (UL) for adults is 3,500 mg per day, a level almost impossible to reach from food alone but achievable with high-dose supplements. Research has shown that the risk of odor increases with higher choline intake.

Other factors can also contribute to a smelly odor after consuming choline:

Intestinal Bacterial Overgrowth: An imbalance in the gut microbiome can lead to an overproduction of TMA, further taxing the liver's detoxification capacity.
Hormonal Fluctuations: For women, hormonal changes around menstruation have been noted to sometimes exacerbate TMAU symptoms.

Dietary Sources of Choline

Choline is naturally found in many foods, with especially high concentrations in animal products. This is why a high-protein diet can sometimes be linked to increased odor issues for sensitive individuals.

Common Food Sources: Eggs, liver, red meat, and certain fish are among the richest dietary sources. Lecithin, a compound found in many foods and supplements, is also broken down into choline by the body.
Vegetable Sources: While lower in concentration, some vegetables, like soybeans and cruciferous vegetables such as broccoli and cauliflower, also contain choline and can contribute to the load.

Comparison of Choline Metabolism and Odor


Feature	Normal Choline Metabolism	Impaired Choline Metabolism (TMAU or Precursor Overload)
FMO3 Enzyme	Fully functional and efficient.	Inactive, deficient, or overwhelmed.
TMA Conversion	Converts TMA to odorless TMAO.	Impairs or prevents conversion of TMA.
Odor	No noticeable fishy odor from urine, sweat, or breath.	Emits a distinct fishy odor in bodily fluids.
Tolerance to Choline	Can tolerate normal to moderately high doses without issue.	Odor can be triggered or worsened by choline-rich foods and supplements.
Cause	Normal metabolic function.	Genetic mutation in FMO3 gene or secondary factors.

Managing the Odor: Dietary and Lifestyle Adjustments

For those affected by choline-induced odor, management typically involves a combination of dietary adjustments and personal hygiene strategies. For most, especially those with acquired or temporary symptoms, these changes can significantly reduce or eliminate the issue.

Here are some management strategies:

Reduce Dietary Choline: Limiting foods high in choline, such as eggs, organ meats, and marine fish, can decrease the amount of TMA produced. However, this should be done with professional guidance to avoid nutrient deficiencies, as choline is essential.
Discontinue High-Dose Supplements: If taking large doses of choline or lecithin supplements, stopping or reducing the amount is often the most direct solution.
Use Low-pH Soaps: Washing with slightly acidic soaps or shampoos (pH 5.5–6.5) can help remove traces of TMA from the skin.
Stay Hydrated: Drinking plenty of water dilutes urine, which can lessen the concentration of odor-causing compounds.
Consult a Healthcare Provider: A doctor can help determine if the odor is caused by TMAU, a liver condition, or other factors and can provide personalized dietary advice. In some cases, short courses of antibiotics or specific supplements like riboflavin (Vitamin B2) may be recommended under medical supervision to alter gut flora and improve metabolic function.

Conclusion

While choline is an important nutrient, the question, "Does choline make urine smell?", has a clear scientific basis. The unpleasant fishy odor is directly linked to the metabolic breakdown of choline into trimethylamine (TMA) and the body's inability to process it into a non-odorous form. For most people, this is a non-issue, but it can be a significant problem for those with the rare genetic disorder trimethylaminuria (TMAU) or those who consume high doses from supplements. By understanding this metabolic pathway, individuals can manage their symptoms effectively through dietary adjustments, supplement awareness, and professional medical guidance.

For more detailed information on trimethylaminuria, consult the National Organization for Rare Disorders (NORD).

Frequently Asked Questions

For most people, the liver enzyme FMO3 efficiently converts the byproduct of choline (trimethylamine, or TMA) into an odorless compound. Those who experience a fishy smell may have a genetic disorder (TMAU) or a temporary metabolic issue that impairs this process, causing TMA to accumulate.

Trimethylaminuria is a rare genetic disorder caused by a mutation in the FMO3 gene. This leads to a deficient FMO3 enzyme, meaning the body cannot break down the strong-smelling TMA, which is then released in sweat, urine, and breath.

Foods rich in choline include eggs, liver, red meat, and some fish. Some vegetables like broccoli, cauliflower, and soybeans also contain choline. The choline in supplements, including lecithin, can also be a factor.

Yes, it is possible. Taking very high doses of choline supplements can overwhelm the body's normal metabolic processes, causing a temporary increase in TMA and a corresponding fishy odor, even in individuals without a diagnosed genetic condition.

To reduce the odor, you can lower your intake of high-choline foods, stop or reduce high-dose supplements, and use low-pH soaps. Staying well-hydrated is also recommended.

Yes, when TMA builds up in the body, it is excreted through multiple bodily secretions, including urine, breath, and sweat, which can all develop a fishy smell.

If you notice a strong fishy odor, especially after starting a supplement, consider reducing or stopping the supplement. However, because choline is an essential nutrient, it's best to consult a healthcare provider or dietitian before making significant dietary changes.