Understanding Why Does L-carnitine Cause Fishy Odor?

October 5, 2025 •

5 min read

While L-carnitine is beneficial for fatty acid metabolism, a peculiar side effect is the development of a fishy body odor in some individuals. This occurs not due to the supplement itself, but because of its complex interaction with specific gut bacteria, highlighting why does L-carnitine cause fishy odor? is a question rooted in our unique internal biology.

Quick Summary

The fishy odor associated with L-carnitine supplementation is caused by the metabolic process in which gut bacteria convert unabsorbed L-carnitine into trimethylamine (TMA). This compound is typically processed by the liver but can build up and be excreted in bodily fluids, causing a strong odor. The phenomenon is linked to an enzyme deficiency or bacterial overgrowth, not the L-carnitine itself.

Key Points

Gut Bacteria Conversion: The fishy odor from L-carnitine is caused by specific gut microbes converting unabsorbed L-carnitine into trimethylamine (TMA).
FMO3 Enzyme Deficiency: Individuals with a genetic condition called trimethylaminuria (TMAU) lack the functional FMO3 enzyme in the liver that normally processes TMA into a non-odorous compound.
High-Dose Overload: Even without a genetic condition, high doses of L-carnitine can produce enough TMA to overwhelm the liver's processing capacity, causing the odor.
Dietary Factors: Omnivorous diets tend to promote the growth of TMA-producing bacteria, increasing the likelihood of this side effect compared to vegan or vegetarian diets.
Mitigation Strategies: Managing the odor can involve reducing the L-carnitine dosage, modifying the diet to lower choline intake, or taking supplements like riboflavin or activated charcoal to aid in TMA processing.
Underlying Health Conditions: Liver or kidney disease can impair the body's ability to clear TMA and TMAO, leading to odor.

The Surprising Journey from L-Carnitine to a Fishy Scent

L-carnitine is a crucial compound for energy production, helping transport long-chain fatty acids into the mitochondria to be burned for fuel. However, what happens to L-carnitine that isn't absorbed by the body is the key to understanding this peculiar side effect. When L-carnitine reaches the large intestine, it becomes a food source for certain types of gut bacteria, which act as the first domino in a chain reaction leading to the fishy odor.

The Role of Gut Microbiota in TMA Production

Specific gut microbes, notably members of the Clostridiales family such as Emergencia timonensis and other bacteria containing the gbu gene cluster, metabolize unabsorbed L-carnitine. This process involves a sequential two-step conversion: first, L-carnitine is converted into an intermediate compound called gamma-butyrobetaine (γBB), and then the γBB is transformed into trimethylamine (TMA). This metabolic pathway is significantly more pronounced in omnivores compared to vegans or vegetarians, as dietary habits influence the composition of the gut microbiota.

How the Liver Typically Handles TMA

Once TMA is produced in the gut, it is absorbed into the bloodstream and travels to the liver. In most healthy individuals, the liver efficiently converts TMA into a non-odorous compound, trimethylamine N-oxide (TMAO), using an enzyme called Flavin-Containing Monooxygenase 3 (FMO3). The TMAO is then excreted harmlessly via the urine. This process ensures that no unpleasant odor is emitted.

The Breakdown: What Causes a Build-up of TMA?

If the TMA is not properly processed by the liver, it can build up and be released in sweat, urine, and breath, producing a strong, fishy smell. There are two main reasons for this buildup:

Genetic Disorder: A rare genetic condition called Trimethylaminuria (TMAU), or “fish odor syndrome,” is caused by a defective FMO3 gene. Individuals with this condition either have a missing or non-functional FMO3 enzyme, preventing the conversion of TMA to TMAO. In some cases, a mild genetic variant can reduce enzyme efficiency, leading to occasional or milder symptoms.
Substrate Overload: Even in individuals with a fully functional FMO3 enzyme, excessively high doses of L-carnitine or other choline-rich foods can overwhelm the liver's capacity to process all the TMA. This saturation can lead to a temporary build-up of TMA, resulting in a transient fishy odor.

Factors Influencing the L-Carnitine and TMA Pathway

Multiple factors play a role in whether an individual will experience this fishy odor when taking L-carnitine supplements:

Dietary Habits: An omnivorous diet, particularly one high in red meat, increases the abundance of TMA-producing bacteria in the gut, making individuals more susceptible to the side effect.
Dosage: The amount of L-carnitine consumed directly impacts the amount of TMA produced. High doses are more likely to overwhelm the system and cause an odor.
Gut Health: The balance of gut bacteria (the microbiome) is critical. A healthy, diverse microbiome may be less prone to producing excessive TMA.
Medical Conditions: Liver or kidney disease can impair the body's ability to process and excrete TMA and TMAO, leading to a buildup.

Managing the Fishy Odor Side Effect

For those who experience the fishy odor, several strategies can help mitigate or eliminate the issue:

Lowering Dosage: Simply reducing the amount of L-carnitine supplement can often resolve the problem by lowering the amount of substrate available for bacterial conversion.
Dietary Adjustments: Decreasing the intake of choline-rich foods, which also contribute to TMA production, may help. Foods to reduce include liver, kidney, eggs, and certain legumes. Conversely, a plant-based diet has been shown to reduce TMAO levels.
Supplementation: Certain supplements can help manage TMA levels. Short courses of antibiotics can reduce gut bacteria populations, while riboflavin (vitamin B2) supplements have been shown to improve symptoms in individuals with TMAU. Activated charcoal can also bind to TMA in the gut and aid in its removal.
Improved Hygiene: Using slightly acidic soaps with a pH between 5.5 and 6.5 can help remove TMA from the skin's surface and reduce the odor.

Comparison of Strategies for Managing Fishy Odor


Strategy	Mechanism	Effectiveness	Potential Drawbacks
Lowering L-Carnitine Dose	Reduces substrate for TMA-producing bacteria.	Highly effective for dose-dependent cases.	May reduce the therapeutic benefits of the supplement.
Dietary Modification	Avoids other TMA precursors like choline.	Moderately effective, especially for genetically predisposed individuals.	Can be restrictive and may require professional guidance to maintain nutritional balance.
Antibiotics (Short-term)	Temporarily reduces TMA-producing gut bacteria.	Can provide quick, temporary relief.	Not a long-term solution; risk of antibiotic resistance and disrupting overall gut health.
Riboflavin Supplementation	Improves the efficiency of the FMO3 enzyme.	Effective for those with genetically related enzyme inefficiency.	Not universally effective for all causes of TMA buildup.
Acidic Soaps	Neutralizes and washes away TMA from skin.	Addresses the symptom (odor) on the body surface.	Does not address the root cause of TMA production.
Activated Charcoal	Absorbs TMA in the gut, preventing absorption.	Can reduce TMA levels in the body.	Can cause constipation and interfere with absorption of other medications and nutrients.

Conclusion: Tailoring Your Approach to Nutrition

In summary, the fishy odor linked to L-carnitine is a metabolic issue resulting from the interaction between gut bacteria and the liver's processing capabilities. It is not an inherent flaw of the supplement itself but rather a sign that the body's natural processing system is either overloaded or compromised, often due to genetic factors related to the FMO3 enzyme. For most people, consuming a standard dose of L-carnitine, or dietary sources of it, will not cause any odor. However, for those who are genetically predisposed to Trimethylaminuria or are taking high doses, the metabolic pathway can be overwhelmed, leading to the noticeable side effect. By adjusting dosage, modifying diet to limit other TMA-precursors like choline, or using targeted supplements like riboflavin and activated charcoal, individuals can effectively manage or eliminate this social discomfort while still benefiting from L-carnitine's properties. Personalizing your nutritional approach based on your body's unique metabolic needs is key to a positive outcome. For more detailed information on TMAU and its management, you can visit the National Organization for Rare Disorders (NORD) website.(https://rarediseases.org/rare-diseases/trimethylaminuria/).

Frequently Asked Questions

The primary cause is the conversion of unabsorbed L-carnitine by certain gut bacteria into trimethylamine (TMA), a compound with a strong fishy odor.

Trimethylaminuria is a genetic metabolic disorder where the liver enzyme (FMO3) that normally processes TMA is deficient. In individuals with TMAU, taking L-carnitine can exacerbate the fishy odor due to the buildup of unmetabolized TMA.

Yes, even in healthy individuals with a normal FMO3 enzyme, taking very high doses of L-carnitine can overwhelm the liver's capacity to process TMA, leading to a temporary fishy odor.

Yes, dietary habits significantly influence the gut microbiome. Diets high in red meat, for instance, are associated with a gut flora that is more efficient at converting L-carnitine to TMA, increasing the risk.

To prevent the odor, you can reduce your L-carnitine dosage, modify your diet to limit other TMA precursors like choline, or supplement with riboflavin or activated charcoal to assist in processing TMA.

Yes, riboflavin (vitamin B2) supplements can improve the function of the FMO3 enzyme for those with genetic deficiencies, while activated charcoal can bind to TMA in the gut and aid in its excretion.

For most people, the odor is a harmless but socially uncomfortable side effect. However, if you suspect a genetic condition like TMAU or have an underlying liver or kidney issue, you should consult a doctor for a proper diagnosis and management plan.