Nearly four out of 10 had cavities, the study on players at eight clubs in England and Wales showed.
The dentists, from the International Centre for Evidence- Based Oral Health at University College London, examined 187 players' sets of teeth.
They found 53 per cent had dental erosion, 45 per cent were bothered by the state of their teeth and seven per cent said it affected their ability to train or play.
Around 40 per cent had tooth decay, compared with 30 per cent of people of a similar age in the general population.
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"There are two main groups - some have a catastrophic effect, they have very severe abscesses that stop them in their tracks and they cannot play or train.
"There'll be others experiencing pain affecting sleeping or sensitivity every time they take a drink.
"At this level of athlete, even small differences can be quite telling."
Nutrition is one of the primary suspects with frequent consumption of sugary or acidic foods during training potentially accounting for tooth decay and erosion.
Needleman said that while "these findings are worrying" clubs were giving dental health a "higher priority" and were educating their players.
Previous research has shown "striking" levels of bad teeth in athletes competing at the London 2012 Olympic Games.
The teeth of athletes at London 2012 were broadly in the same state as those of footballers.
Players from Manchester United, Hull, Southampton, Swansea, West Ham, Brighton, Cardiff and Sheffield United all took part in the study.
"Oral health is an area where many athletes have greater problems than the general population so it has been a massive achievement for so many professional football clubs to collaborate with each other to help us understand the scale of this problem better," Stijn Vandenbroucke, the head of medicine and sports science at West Ham, said.