The 47-count indictment unsealed in a federal court in New York charged the defendants with racketeering, wire fraud and money laundering conspiracies as part of a scheme that spanned more than two decades, the U.S. Department of Justice said in a statement.
"The indictment alleges corruption that is rampant, systemic, and deep-rooted both abroad and here in the United States," U.S. Attorney General Loretta Lynch said in the statement.
"It spans at least two generations of soccer officials who, as alleged, have abused their positions of trust to acquire millions of dollars in bribes and kickbacks," she added.
Seven FIFA officials, including current FIFA vice president and executive committee member Jeffrey Webb, were arrested by Swiss authorities on Wednesday and detained pending extradition to the United States, the department said.
The arrests were made shortly after dawn at a Zurich hotel where officials are staying ahead of this week's FIFA presidential election.
FIFA president Sepp Blatter was not among those arrested nor was he charged, according to Swiss and U.S. justice officials.

Some of the figures indicted in the FIFA corruption controversy
Eduardo Li (Costa Rica)
Eduardo Li, 56, is a FIFA executive committee member elect and a CONCACAF executive committee member. He is the Costa Rican Football Federation (FEDEFUT) president.
Mr Li is the former president of CONMEBOL, the South American football federation and footballer.
Jack Warner (Trinidad and Tobago)
Jack Warner is a former FIFA vice president and president of CONCACAF. He resigned from theses posts in 2011. Mr Warner joined the FIFA executive committee in 1983.
In April 2013, The Confederation of North, Central American and Caribbean Association Football (CONCACAF) said in its Integrity Committee report on CONCACAF during Warner’s presidency that Warner committed fraud against CONCACAF and FIFA.
Mr Warner is a former national security minister of Trinidad and Tobago.
José Maria Marin (Brasil)
José Maria Marin, 83, is a member of the FIFA organising committee for Olympic football tournaments. Mr Marin, a former football player, was president of the Brazilian Football Confederation (CBF) between March 2012 and April 2015.
The CBF gave out controversial £16,000 ($A32,000) Parmigiani watches at its congress in Sao Paulo in 2014.
Before that he was vice-president of the Brazilian Football Confederation (2008-2012).
Marin was the 26th São Paulo state governor between 1982 and 1983.
Costas Takkas (Cayman Islands)
Costa Takkas, 58, is the attache to the Confederation of North, Central American and Caribbean Association Football (Concacaf) president.
He is the former general secretary of the Cayman Island Football Association.
Eugenio Figueredo (Uruguay)
Eugenio Figueredo, 83, is the vice-president and executive committee member of FIFA.
Mr Figueredo was president of the South American Football Confederation (CONMEBOL) between 2013 and 2014, and served as president of the Uruguayan Football Federation (AUF).
He was arrestesd in Zurich.
Jeffrey Webb (Cayman Islands)
Jeffrey Webb is FIFA vice president and president of CONCACAF.
Mr Webb, 50, is also president of the Cayman Islands Football Association. He was born and lives in the Cayman Islands.
He was arrested by the Swiss police.
Julio Rocha (Nicaragua)
Julio Rocha is a FIFA development officer. Mr Rocha was formerly president of the Nicaraguan Football Federation (FENIFUT) and Central American Football Union (UNCAF).
He was arrested in Zurich.
Nicolás Leoz (Paraguay)
Nicolás Leoz is a former president of CONMEBOL (South American Football Confederation) between 1986 and 2013 and FIFA executive committee member. Mr Leoz stood down from both posts in April 2013.
Before that, he was president of the Paraguayan Football Association (1971–1973 and 1979–1985).
Rafael Esquivel (Venezuela)
Rafael Esquivel, 68, has been the president of the Venezuelan Football Federation (FVF) since 1988.
Mr Esquivewl is an executive committee member of CONMEBOL. He was arrested by the Swiss police over the corruption allegations.
The Ethics Committee of FIFA notified the FVF on Wednesday that it had suspended Mr Esquivel from his post following the FIFA corruption probe.
Case continues
Authorities also began executing a search warrant at the Miami, Florida, headquarters of the Confederation of North, Central American and Caribbean Association Football (CONCACAF) on Wednesday morning, the department said.
Separately to Wednesday's arrests, four individuals and two corporate defendants have already pleaded guilty to various charges in the case, the department said.
Three of the men had entered guilty pleas as early as July 2013, according to the department.
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