Essendon will fight the disrepute charges brought against the club, its coach James Hird and three other senior club officials over the Bombers' supplements scandal.
While the AFL charged the club and its officials, the Essendon players do not face anti-doping charges - for now.
Only minutes after AFL general counsel Andrew Dillon made the announcement on Tuesday night, Essendon chairman Paul Little said the charges "will be vigorously defended".
The AFL Commission is scheduled to hear the charges on August 26 and it can issue crippling penalties, including stripping Essendon of its premiership points this season, taking away draft picks and issuing heavy fines.
Individuals also face suspension if the commission finds them guilty.
But there has also been speculation that now the AFL has laid charges, court injunctions could be issued.
Hird, club doctor Bruce Reid, football manager Danny Corcoran and assistant coach Mark Thompson were all charged.
"The club and each person are all charged with engaging in conduct that is unbecoming or likely to prejudice the interests or reputation of the AFL or to bring the game of football into disrepute," Dillon said in his statement.
The AFL's decision to lay charges is the latest development in a saga that started on February 5, when Essendon announced they would come under Australian Sports Anti-Doping Authority (ASADA) and AFL investigation.
The crisis surrounds last year's supplements program at the club.
But Dillon's much-anticipated announcement had some good news for Essendon.
He said at this stage, it did not appear that ASADA would charge any players with anti-doping offences.
The AFL laid the charges after considering an interim ASADA report on Essendon.
ASADA's beefed-up powers, which took effect on August 1, mean the anti-doping body is continuing its investigation into the club and there is no indication when it will end.
Dillon said there did not appear to be any specific anti-doping violation related to the anti-obesity drug AOD-9604, a drug at the centre of the crisis, or any other banned substance.
"As such, at the present time, no infraction notices will be issued under the AFL anti-doping code." Dillon added.
Dillon also noted that the ASADA and AFL investigations remain open and further charges could be laid.
There was speculation that if captain Jobe Watson was charged and convicted, he could be stripped of last year's Brownlow Medal.
Little admitted that the Bombers had made mistakes, but they would defend themselves.
"Essendon takes these matters very seriously," Little said in a statement.
"They are based on assertions contained in an interim report from ASADA and will be vigorously defended.
"Essendon welcomes the news that no infraction notices have been issued against any of its players and the AFL's statement that, on current evidence, no notices will be issued.
"There is no doubt the club and individuals have made mistakes and that our governance and people management had significant gaps ... we have also implemented fundamental reforms."
Essendon also released a statement from Watson on behalf of the team.
"As we've said all along, none of us believed we'd done anything wrong in relation to the 2012 supplements program," Watson said.
"We've fully co-operated with every part of the ASADA investigation and we've always said we've got nothing to hide ... we feel vindicated by this announcement."
The strain of the crisis has proved too much for the team over the last three weeks.
After a strong season, they have suffered heavy losses to Hawthorn, Collingwood and West Coast and dropped out of the top four.
They should still make the finals, but only if they are allowed to keep their premiership points.
The AFL finals will start on September 6 and the commission hearing means ninth spot on the ladder is the goal for several teams outside the eight.
Essendon's crisis has already had a massive effect on the club.
They sacked high performance manager Dean Robinson and sports scientist Stephen Dank, who have threatened to take legal action.
Chief executive Ian Robson resigned after a damning independent review of the club's governance.
Chairman David Evans dramatically collapsed in the team dressing rooms after the Hawthorn loss and resigned the next night.
The AFL received the interim ASADA report on August 2 and there had been rising speculation since about possible charges.
On Tuesday morning, Hird continued to vehemently protest his innocence and defend the club.
"I think we all find it hard to believe that charges can be laid on individuals or the club when none of our players have (been) shown to take performance-enhancing drugs, none of our players have shown that they've been harmed by anything that's been given," he said.
"And we're dealing with an interim report - the report's not finalised.
"We're all sitting back staggered and shocked that any charges could possibly be laid on those points."
