The Freedom from Religion Foundation (FFRF) sued the IRS in a federal district court in Wisconsin, claiming that 501(c)(3) tax code provisions make it easier for churches to obtain and maintain tax-exempt status than other nonprofit organizations. This, they claim, violates the First Amendment's prohibition of an "establishment of religion" and the Fifth Amendment's guaranty of the equal protection of the laws. Freedom from Religion Foundation v. Werfel, 2013 WL 4501057 (W.D. Wis. 2013).

In particular, FFRF alleged that it was required to file a "detailed application" (Form 1023) and pay a fee before obtaining tax exempt status, and since then has been required to file "detailed, intrusive and expensive annual reports" (Form 990) in order to maintain that status, but churches are not required to do either of these things.

The federal government, which defended the constitutionality of the tax code provisions (since they are federal statutes), asked the court to dismiss the lawsuit on the ground that FFRF lacked "standing" to pursue its claims. Standing is a requirement of any plaintiff in a federal case. It has been described by the United States Supreme Court as follows:

The party who invokes the power [of the federal courts] must be able to show not only that the statute is invalid, but that he has sustained or is immediately in danger of sustaining some direct injury as a result of its enforcement, and not merely that he suffers in some indefinite way in common with people generally. Doremus v. Board of Ed. of Hawthorne, 342 U.S. 429 (1952).