The study, conducted by researchers at Osaka University in Japan found that parts of cocoa beans, the main ingredient of chocolate, thwart mouth bacteria and tooth decay.
They found that the cocoa bean shell - the outer part of the bean that usually goes to waste in chocolate production - has anti-bacterial effect on the mouth and can fight effectively against plaque and other damaging agents.
Tooth decay occurs when bacteria in the mouth turn into acid, which damages the surface of the teeth and cause cavities.
Japanese scientists have discovered that chocolate is not less harmful than many other sweet foods, as antibacterial agents in cocoa beans offset high levels of sugar.
After three months, the study found that the rates with a high sugar diet had 14 holes on average compared to just six cavities than those who received skin cocoa beans in their diet.
The researchers now plan to test their findings in humans.
Speaking to New Scientist magazine, Takashi Ooshima, Osaka University, said their findings could lead to new treatments for tooth decay.
"It may be possible to use mouthwash CBH extracts, or supplements for a toothpaste."
It could even be put back into the chocolate to make it better for the teeth, he said
"They certainly have an effect but good oral hygiene, rather than eating lots of chocolate, is the way to good healthy teeth."
A spokesman for the British Dental Association said: "If it's true that chocolate does help reduce tooth decay and cavities which can only be a good thing, but you have to remember that chocolate contains sugar.
"Our advice remains the same: if people want to eat candy and sweet drinks they should limit it, and visit your dentist regularly."
Sources: BBC News