Bosch is the founder of the Biogenesis clinic, the center of baseball's most recent doping scandal.
Rodriguez's lawyers said MLB officials have begun a "witch hunt" to force him out of baseball. They also claim the MLB gave Bosch $5 million to cooperate with the proceedings, and paid $150,000 in cash for records related to Rodriguez, which were apparently stolen.
The suit cites "at least one individual who claims to have knowledge of Mr. Bosch's deal."
A portion of the cash “was handed off in a bag at a Fort Lauderdale, Fla.-area restaurant,” the lawsuit says.
A-Rod suit: Selig, MLB have "persistently employed powers not available to them .. in order to make an example of Mr. Rodriguez."— Bill Shaikin (@BillShaikin) October 4, 2013
"This matter is entirely separate from the ongoing arbitration," Rodriguez said in a statement.
"I look forward to the arbitration proceedings continuing, and for the day to come when I can share my story with the public and my supporters."
Major League Baseball issued a statement on the lawsuit shortly after it was filed early Thursday.
"While we vehemently deny the allegations in the complaint, none of those allegations is relevant to the real issue: whether Mr. Rodriguez violated the Joint Drug Prevention and Treatment Program by using and possessing numerous forms of prohibited performance-enhancing substances, including testosterone and human growth hormone, over the course of multiple years and whether he violated the Basic Agreement by attempting to cover-up his violations of the Program by engaging in a course of conduct intended to obstruct and frustrate the Office of the Commissioner's investigation," the statement read.
See the full text of the lawsuit here.