When asked by BBC Sport about Chelsea and Manchester City, it confirmed an investigation was "ongoing". City have no knowledge of an investigation and are adamant they have done nothing wrong, while Chelsea insist they "comply with all Fifa statutes ...
Chelsea are being investigated by Fifa for the third timeChelsea and Manchester City are being investigated by Fifa over their recruitment of young players.
This is the third time football's world governing body has looked at Chelsea, and in 2009 they were banned from making signings for two years.
In May, the Premier League fined City £300,000 and banned them from signing academy players for two years.
Fifa has stringent rules in place for signing players under the age of 18 to prevent exploitation and trafficking.
When asked by BBC Sport about Chelsea and Manchester City, it confirmed an investigation was "ongoing".
City have no knowledge of an investigation and are adamant they have done nothing wrong, while Chelsea insist they "comply with all Fifa statutes and regulations when recruiting players".
In 2009, Chelsea were banned from signing players after being found guilty of inducing Gael Kakuta to break his contract with Lens, though the sanction was lifted on appeal.
They were also scrutinised last year for the 2014 signing of Bertrand Traore from Association Jeunes Espoirs De Bobo-Dioulasso.
City's punishment, meanwhile, came after they were found to have approached the family of two young players who were registered with other clubs.
They are also awaiting a verdict from the Court of Arbitration for Sport over their signing of 16-year-old midfielder Benjamin Garre from Argentine club Velez Sarsfield in 2016.
Fifa cleared City of Sarsfield's allegation that they were not allowed to sign the player because of his nationality, on the basis Garre had an Italian passport.
However, the club opted to take the matter further, and the case was heard at the beginning on July.
In January last year, both Real Madrid and city rivals Atletico were banned from signing players for two transfer windows after breaching Fifa rules relating to the signing of minors.
Real had the sanction halved on appeal but Atletico had theirs upheld by the Court of Arbitration for Sport.
Fifa's rules on the transfer of under-18s
Fifa bans the transfer of under-18s to different countries unless they meet strict criteria. It brought in the rules to help protect children from exploitation and trafficking.
Under-18s can only be transferred abroad if:
The player's parents move to the country in which the new club is located for non-footballing reasons.
Both clubs are in the European Union or European Economic Area and the player is aged between 16 and 18. Even then, the buying club must meet more criteria relating to education, training, living conditions and support.
They live within 100km of the club.
Analysis - 'This won't be the last time'
BBC Sport's Simon Stone
Chelsea and Manchester City are adamant they have done nothing wrong, but in merely admitting investigations are ongoing, Fifa is again shining a light on the recruitment of young players.
Chelsea and City have established themselves as having the best young players in England. Chelsea have won the past four FA Youth Cups, beating City in the past three finals.
But it would be naive to think outstanding young players arrive at those clubs by chance.
Huge amounts of time and resource are put into recruitment, both at home and abroad.
As the cases of City and Liverpool proved when they were fined by the Premier League last season, clubs do not always play by the rules. And English clubs are not operating in a vacuum.
As the professional desire and financial incentives for winning increase, even if Fifa's latest probe unearths nothing, it is fair to assume it won't be the last time they will feel the need to make sure regulations are not being broken.
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