A study in the journal Nature Medicine showed that carnitine in red meat was broken down by bacteria in the gut.
This kicked off a chain of events which resulted in higher levels of cholesterol and an increased risk of heart disease.
Dieticians warned there may be a risk to people taking carnitine supplements.
There has been a wealth of studies suggesting that regularly eating red meat may be damaging to health.
In the UK, the government recommends eating no more than 70g of red or processed meat a day - the equivalent of two slices of bacon.
Saturated fat and the way processed meat is preserved are thought to contribute to heart problems. However, this was not thought to be the whole story.
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Experiments on mice and people showed that bacteria in the gut could eat carnitine.
Carnitine was broken down into a gas, which was converted in the liver to a chemical called TMAO.
In the study, TMAO was strongly linked with the build-up of fatty deposits in blood vessels, which can lead to heart disease and death.
Dr Hazen, from the Cleveland Clinic, said TMAO was often ignored: "It may be a waste product but it is significantly influencing cholesterol metabolism and the net effect leads to an accumulation of cholesterol.
"The findings support the idea that less red meat is better.
"I used to have red meat five days out of seven, now I have cut it way back to less than once every two weeks or so."
He said the findings raised the idea of using a probiotic yogurt to change the balance of bacteria in the gut.
Reducing the number of bacteria that feed on carnitine would in theory reduce the health risks of red meat.
Vegetarians naturally have fewer bacteria that are able to break down carnitine than meat-eaters.