As with all aspects of a federal criminal prosecution, there are certain procedures that must be followed during the course of an investigation that could result in an indictment. The procedures are not optional or discretionary, and can provide valuable grounds for defenses if the case ends up in the courtroom. The federal antitrust statutes make it the duty of the United States attorneys to prosecute antitrust violations, and place investigative authority with the Department of Justice.

The Antitrust Division is required to send a target letter to the subject of their investigation. This letter simply informs the person that he or she is the target of an ongoing investigation, and is meant to give fair notice and the opportunity to retain counsel. Generally the Antitrust Division will prosecute crimes relating to the integrity of the investigative process (such as obstruction of justice and perjury), as well as other substantive offenses related to the antitrust violation (such as mail fraud or money laundering). Just as suspected antitrust violations are referred to the Antitrust Division by other agencies, the Division will refer suspected criminal activities in other areas to the appropriate agency. For example, if an antitrust investigation uncovers evidence of tax evasion, the Antitrust Division will refer their findings to the IRS for further investigation.