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The Internal Revenue Service has been auditing how the firm allocates profits among countries and jurisdictions.
But Microsoft said "the issues raised by the IRS are relevant to the past but not to our current practices".
In a securities filing, Microsoft said the IRS was seeking an additional tax payment of $28.9bn plus penalties and interest.
Other American tech firms such as Amazon and Facebook have also faced similar calls to pay more taxes.
In June, it agreed to pay $20m to the Federal Trade Commission (FTC) after the company was found to have illegally collected data on children who had started Xbox accounts.
But the firm may soon have a victory over its plan to buy Activision Blizzard, which makes Call of Duty, for $68.7bn as the deal is expected to be finalised soon.