It is so successful in combating decay that scientists believe some of its components may one day be added to mouthwash or toothpaste.
A study carried out by researchers at Osaka University in Japan found that parts of the cocoa bean, the main ingredient of chocolate, thwart mouth bacteria and tooth decay.
They discovered that the cocoa bean husk - the outer part of the bean which usually goes to waste in chocolate production - has an 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 sugar to acids, which eat away at the tooth's surface and cause cavities.
The Japanese scientists found that chocolate is less harmful than many other sweet foods because the antibacterial agents in cocoa beans offset its high sugar levels.
They tested their theory on rats by adding an extract of cocoa bean husk (CBH) to their drinking water. Another group was infected with streptococcus mutans bacteria, which contributes to plaque and tooth decay. They were also fed a high-sugar diet.
After three months, the study found that the rates with the high sugar diet had 14 cavities on average compared to just six cavities for those who received cocoa bean husk in their diet.
The researchers are now planning to test their findings on humans.
Speaking to New Scientist magazine, Takashi Ooshima, from Osaka University, said their findings could lead to new treatments for tooth decay.
"It may be possible to use CBH extract in a mouthwash, or supplement it to a toothpaste."
It could even be put back into chocolate to make it better for teeth, he said.
"They certainly have effects but good oral hygiene, rather than eating lots of chocolate, is the way to good healthy teeth."
A spokeswoman for the British Dental Association said: "If it's true that chocolate does help reduce dental decay and cavities that can only be a good thing, but you must remember that chocolate contains sugar.
"Our advice remains the same: if people want to eat sugary sweets and drinks they should limit them to meal times, and visit their dentist regularly."