As generally understood, a law that is ex post facto—literally, after the fact—is one that criminally punishes conduct that was lawful when it was done. It is an aspect of the fundamental maxim, nulla poena sine lege: there can be no punishment without law—in this case, without preexisting law. Despite the fact that the prohibition against such laws had worked its way into English law (as celebrated by Sir William Blackstone), Parliament had, nonetheless, claimed the right to enact ex post facto laws in the form of bills of attainder against unpopular groups and persons. In addition, prior to the Constitutional Convention, some states themselves had passed ex post facto laws. (The prohibition of ex post facto state laws is found in Article I, Section 10, Clause 1.)

Nevertheless, opposition to ex post facto laws was a bedrock principle among the Framers. In The Federalist No. 78, Alexander Hamilton noted that "the subjecting of men to punishment for things which, when they were done, were breaches of no law" is among "the favorite and most formidable instruments of tyranny." Thomas Jefferson noted in an 1813 letter to Isaac McPherson "the sentiment that ex post facto laws are against natural right."

In Philadelphia, the Framers debated the issue vigorously. Some thought an explicit ban on ex post facto laws an absolute necessity. Others, such as Oliver Ellsworth of Connecticut, echoed the natural law tradition and "contended that there was no lawyer, no civilian who would not say that ex post facto laws were void of themselves. It cannot then be necessary to prohibit them." James Wilson declared that the prohibition against ex post facto laws in the state constitutions had been ineffective and would be likewise "useless" in the national constitution. Hugh Williamson then pointed to North Carolina's prohibition of ex post facto laws. He acknowledged that the prohibition had been violated, but argued that "it has done good there & may do good here, because the Judges can take hold of it." The delegates then approved the clause, seven states to three.

Later, James Dickinson reported that, on examining Blackstone's Commentaries on the Laws of England, he found that "the terms ‘ex post facto' related to criminal cases only; that they would not consequently restrain the states from retrospective laws in civil cases and that some further provision for this purpose would be requisite." After the Committee of Style had reported the ex post facto law clauses in their current form, George Mason of Virginia moved to strike the prohibition against ex post facto laws because the clause might apply to civil laws "and no Legislature ever did or can altogether avoid them in Civil cases." Elbridge Gerry seconded the motion because he wanted a clearer statement that prohibition did in fact apply to "Civil cases." Mason's motion was unanimously rejected.

The Court addressed the issue of the scope of the clause in one of its earliest constitutional decisions. Calder v. Bull, decided in 1798, involved a determination by the Connecticut legislature that a judicial decree should be set aside and a new trial held regarding a contested will. Without dissent, the Court held that the Connecticut legislature's action was not an ex post facto law forbidden under Article I, Section 10. Justice Samuel Chase defined ex post facto laws as:

1st. Every law that makes an action done before the passing of the law, and which was innocent when done, criminal; and punishes such action. 2d. Every law that aggravates a crime, or makes it greater than it was, when committed. 3d. Every law that changes the punishment, and inflicts a greater punishment, than the law annexed to the crime, when committed. 4th. Every law that alters the legal rules of evidence, and receives less, or different testimony, than the law required at the time of the commission of the offence, in order to convict the offender. All these, and similar laws, are manifestly unjust and oppressive.

Chase also made the point that, had the ex post facto law clauses barred all retroactive civil laws, the prohibition on the impairment of contracts by states (Article I, Section 10, Clause 1) and on uncompensated takings by the federal government (the Fifth Amendment's Takings Clause) would have been unnecessary.

Although some believe that the question of the scope of the Ex Post Facto Clause had not been squarely presented in Calder v. Bull, the Supreme Court adopted and upheld Justice Chase's position in Carpenter v. Pennsylvania (1855). Since that time, a few commentators and two Justices, William Johnson in Satterlee v. Matthewson (1829) and Clarence Thomas in Eastern Enterprises v. Apfel (1998), have voiced doubt over the accepted rule that the Ex Post Facto Clause applies only to criminal legislation. In Apfel, citing Justice Joseph Story, Thomas contended that the Ex Post Facto Clause, even more clearly than the Takings Clause, reflects the principle that retrospective laws are "generally unjust." He continued:

Since Calder v. Bull,...this Court has considered the Ex Post Facto Clause to apply only in the criminal context. I have never been convinced of the soundness of this limitation, which in Calder was principally justified because a contrary interpretation would render the Takings Clause unnecessary....In an appropriate case, therefore, I would be willing to reconsider Calder and its progeny to determine whether a retroactive civil law that passes muster under our current Takings Clause jurisprudence is nonetheless unconstitutional under the Ex Post Facto Clause.

The weight of precedent and scholarly opinion, however, supports Justice Chase's view.

While the Supreme Court has hewn to the position that the Ex Post Facto Clause prohibits criminal penalties only, it has also applied the clause in civil cases where criminal penalties are disguised as civil disabilities. As the Court has said, "it is the effect, not the form, of the law that determines whether it is ex post facto." Weaver v. Graham (1980).

When undertaking this inquiry, courts assess whether the ostensibly civil fine or penalty is penal in nature. As Justice Felix Frankfurter articulated the inquiry:

The mark of an ex post facto law is the imposition of what can fairly be designated punishment for past acts. The question in each case where unpleasant consequences are brought to bear upon an individual for prior conduct, is whether the legislative aim was to punish that individual for past activity, or whether the restriction of the individual comes about as a relevant incident to a regulation of a present situation, such as the proper qualifications for a profession. De Veau v. Braisted (1960).

The issue of what constitutes "punishment" involves other clauses of the Constitution as well. For example, recent interpretations of the Double Jeopardy Clause of the Fifth Amendment may have implications for the Ex Post Facto Clause. In United States v. Halper (1989), the Supreme Court said that if "civil proceedings...advance punitive as well as remedial goals," they do not constitute punishment that is prohibited under the Double Jeopardy Clause. In United States v. Ursery (1996), the Court found that confiscating the home of an individual convicted for growing marijuana was a "civil remedial sanction" rather than a civil penalty. On the other hand, the Court has found that an imposed forfeiture constitutes a punitive sanction under the Eighth Amendment's excessive fines clause. United States v. Bajakajian (1998).

Most recently, in Smith v. Doe (2003), the Court (by a 6–3 decision) rejected the claim that Alaska's sex offender registration and notification law constituted retroactive punishment forbidden by the Ex Post Facto Clause (of the analogue Article I, Section 10, Clause 1). The Court focused on the legislature's "intention" and applied the following analytical framework:

If the intention of the legislature was to impose punishment, that ends the inquiry. If, however, the intention was to enact a regulatory scheme that is civil and nonpunitive, we must further examine whether the statutory scheme is so punitive either in purpose or effect as to negate [the State's] intention to deem it civil. Because we ordinarily defer to the legislature's stated intent, only the clearest proof will suffice to override legislative intent and transform what has been denominated a civil remedy into a criminal penalty.

A possible problem with the Court's current interpretation of the Ex Post Facto Clause is the fact that many criminal laws could be rephrased as civil. As currently understood, the Ex Post Facto Clause thus guards against only the most severe use of the legislature's power to make laws retroactive. They do so effectively where personal liberty is at issue. But the clause is of little use to those who are aggrieved by most forms of retroactive civil legislation, which frequently affect property rights of one form or another.

The clause applies only to criminal statutes, not judicial decisions having a retroactive effect. Retroactive judicial decisions, however, can be challenged under the Due Process Clause. See Rogers v. Tennessee (2001). Retroactive procedural statutes that work to deny a defense, bar the practice of law, increase punishment, or increase the likelihood of conviction may violate the Ex Post Facto Clause. See Cummings v. Missouri (1867); Ex parte Garland (1867); Carmell v. Texas (2000). In Stogner v. California (2003), the Court struck down a California law that revived prosecutions for sexual abuse of children after the statute of limitations had expired.

A statutory increase in punishment is also an impermissible ex post facto law. Collins v. Youngblood (1990). The clause prohibits, for example, applying new sentencing guidelines to a defendant who committed the crime prior to their promulgation, Miller v. Florida (1987); or canceling early-release credits after they have been awarded, Lynce v. Mathis (1997); but not a retroactive decrease in the availability of parole hearings, California Department of Corrections v. Morales (1995); nor a change in the place of trial, Cook v. United States (1891); nor deportation, Mahler v. Eby (1924). The Court found no increase in punishment in a change of method of execution from hanging to electrocution, Malloy v. South Carolina (1915); or in imposing civil commitment on a sexual predator after sentence, Kansas v. Hendricks (1997).