Criminal Justice Integrity and Innocence Protection Act of 2001 - Amends the Federal criminal code to establish procedures for post-conviction DNA testing in Federal court. Requires the applicant to: (1) assert actual innocence of the offense for which the applicant was convicted or of uncharged conduct if exoneration of such conduct would result in a mandatory reduction in sentence; (2) identify the specific evidence to be tested and a theory of defense, not inconsistent with previously asserted theories, that the requested DNA testing would support; and (3) present a prima facie showing that the perpetrator's identity was at issue in the trial and that DNA testing would establish the applicant's innocence.

Sets forth provisions regarding court order requirements, testing procedures, time limitations in capital cases, post-testing procedures, applicability of Federal habeas corpus, and appointment of counsel for an indigent applicant.

Prohibits the Government from destroying biological material preserved if specified conditions apply. Authorizes the court to impose sanctions for intentional violations.

Amends the State Justice Institute Act of 1984 to: (1) authorize the State Justice Institute to award grants to States to assist in the adoption of national minimum standards for competent counsel in non-Federal capital cases; and (2) direct the Institute to establish such standards and report annually to Congress and the Attorney General detailing the status of capital defense in each State that provides for capital punishment.