There are three main exceptions to the sovereign immunity of a state. First, The Eleventh Amendment does not stop a federal court from issuing an injunction against a state official who is violating federal law. Although the state official may be abiding by state law, he is not permitted to violate federal law, and a federal court can order him to stop the action with an injunction.[ Ex Parte Young, 209 U.S. 123 (1908) ] Money damages are possible against the state officer, as long as the damages are attributable to the officer himself, and are not paid from the state treasury. Scheuer v. Rhodes, 416 U.S. 232 (1974).

The Eleventh Amendment does not automatically protect political subdivisions of the state from liability. Moor v. County of Alameda, 411 U.S. 693 (1973). The main factor is whether the damages would come out of the state treasury. Hess v. Port Authority Trans-Hudson Corp., 115 S. Ct. 394 (1994), If the state would have to pay for damages from the state treasury, then the Eleventh Amendment will serve as a shield from liability. Other factors may include the amount of state control and how state law defines the subdivision, although the Supreme Court has never issued a comprehensive guideline. Eleventh Amendment immunity does not protect municipal corporations or other governmental entities that are not political subdivisions of the state, such as cities, counties, or school boards.

Finally, the states surrendered a portion of the sovereign immunity that had been preserved for them by the Constitution when the Fourteenth Amendment was adopted. Therefore, Congress may authorize private suits against non- consenting states to enforce the constitutional guarantees of the Fourteenth Amendment. The Eleventh Amendment is a constitutional limit on federal subject matter jurisdiction, and Congress can override it by statute only pursuant to the § 5 enforcement power of the Fourteenth Amendment.