The researchers analysed four isolated but associated mandibular teeth on the left side of the Neanderthal's mouth.
The teeth were found more than 100 years ago at Krapina site in Croatia, which was originally excavated between 1899- 1905.
In the recent years, researchers have reexamined many items collected from the site.
"As a package, this fits together as a dental problem that the Neanderthal was having and was trying to presumably treat itself, with the toothpick grooves, the breaks and also with the scratches on the premolar," said David Frayer, professor at from University of Kansas in the US.
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Researchers analysed the teeth with a light microscope to document occlusal wear, toothpick groove formation, dentin scratches, and ante mortem, lingual enamel fractures.
Even though the teeth were isolated, previous researchers were able to reconstruct their order and location in the male or female Neanderthal's mouth.
Frayer said researchers have not recovered the mandible to look for evidence of periodontal disease, but the scratches and grooves on the teeth indicate they were likely causing irritation and discomfort for some time for this individual.
"The scratches indicate this individual was pushing something into his or her mouth to get at that twisted premolar," Frayer said.
The features of the premolar and third molar are associated with several kinds of dental manipulations, he said.
Mostly because the chips of the teeth were on the tongue side of the teeth and at different angles, the researchers ruled out that something happened to the teeth after the Neanderthal died.
They did not identify what the Neanderthal would have used to produce the toothpick grooves, but it possibly could have been a bone or stem of grass.
"It's maybe not surprising that a Neanderthal did this, but as far as I know, there's no specimen that combines all of this together into a pattern that would indicate he or she was trying to presumably self-treat this eruption problem," he said.
The study was published in the journal Bulletin of the International Association for Paleodontology.
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