Mutations in the FMO3 gene cause trimethylaminuria. This gene provides instructions for making an enzyme that breaks down nitrogen-containing compounds from the diet, including trimethylamine. This compound is produced by bacteria in the intestine during the digestion of proteins from eggs, liver, legumes (such as soybeans and peas), certain kinds of fish, and other foods. Normally, the FMO3 enzyme converts strong-smelling trimethylamine into another molecule that has no odor. If the enzyme is missing or its activity is reduced because of a mutation in the FMO3 gene, trimethylamine is not processed properly and can build up in the body. As excess trimethylamine is released in a person's sweat, urine, and breath, it causes the odor characteristic of trimethylaminuria. Researchers believe that stress and diet also play a role in triggering symptoms.

Although FMO3 gene mutations account for most cases of trimethylaminuria, the condition can also be caused by other factors. The strong body odor may result from an excess of certain proteins in the diet or from an abnormal increase in bacteria that produce trimethylamine in the digestive system. A few cases of the disorder have been identified in adults with liver or kidney disease. Temporary symptoms of this condition have been reported in a small number of premature infants and in some healthy women at the start of menstruation.