The Supreme Court's decision upheld Congress's ban and held that it did not impose an undue burden on the due process right of women to obtain an abortion, "under precedents we here assume to be controlling",[2] such as the Court's prior decisions in Roe v. Wade and Planned Parenthood v. Casey.

Gonzales was widely interpreted as signaling a shift in Supreme Court jurisprudence toward a restriction of abortion rights, occasioned in part by the retirement of Sandra Day O'Connor and her replacement by Samuel Alito.

[13] Justice Anthony Kennedy wrote for the Court that the respondents had failed to prove that Congress lacked authority to ban this abortion procedure.

The Court left the door open for as-applied challenges, citing its recent precedent in Ayotte v. Planned Parenthood of New England.

According to Washington Post reporter Benjamin Wittes, "The Court majority, following the path it sketched out last year in the New Hampshire case, decided to let the law stand as a facial matter and let the parties fight later about what, if any, applications need to be blocked.

The concurrence also stated that Justices Thomas and Scalia joined the Court's opinion "because it accurately applies current jurisprudence."

Referring in particular to Planned Parenthood v. Casey, Ginsburg sought to ground the Court's abortion jurisprudence based on concepts of personal autonomy and equal citizenship rather than the Court's previous privacy approach: "Thus, legal challenges to undue restrictions on abortion procedures do not seek to vindicate some generalized notion of privacy; rather, they center on a woman's autonomy to determine her life's course, and thus to enjoy equal citizenship stature.

"[5] Observing that the majority opinion in Carhart did not touch upon the question of whether the Court's prior decisions in Roe v. Wade and Planned Parenthood v. Casey were valid, Justice Ginsburg wrote, "Casey's principles, confirming the continuing vitality of 'the essential holding of Roe,' are merely 'assume[d]' for the moment ... rather than 'retained' or 'reaffirmed.'"

She concluded by criticizing the majority for abandoning the principle of stare decisis, writing that "a decision so at odds with our jurisprudence should not have staying power."