Since the adoption of the Bill of Rights in 1791, the government has been prohibited from gathering evidence for use in a prosecution against an American citizen in a courtroom unless the government could prove the existence of probable cause that a crime has been committed. The hard won legislative compromise previously embodied in FISA reduced the probable cause requirement only for national security intelligence gathering. The Patriot Act effectively eliminates that compromise by allowing the Executive Branch to bypass the Fourth Amendment in gathering evidence for a criminal prosecution.

Judge Aiken wasn't having it:

The Fourth Amendment ordinarily requires that the subject of a search be notified that the search has occurred. Although in some circumstances the government is permitted to delay the provision of notice, the Supreme Court has never upheld a statute that, like FISA, authorizes the government to search a person's home or intercept his communications without ever informing the person that his or her privacy has been violated. Except for the investigations that result in criminal prosecutions, FISA targets never learn that their homes or offices have been searched or that their communications have been intercepted. Therefore, most FISA targets have no way of challenging the legality of the surveillance or obtaining any remedy for violations of their constitutional rights.

FISA also does not require particularity. The Fourth Amendment prohibits the government from conducting intrusive surveillance unless it first obtains a warrant describing with particularity the things to be seized as well as the place to be searched.

Judge Aiken also concluded that the Patriot Act's authorization of unreasonably long (120 day) surveillance orders violated the Fourth Amendment.

Here's the good stuff:

Finally and perhaps most significantly, In re Sealed Case ignores congressional concern with the appropriate balance between intelligence gathering and criminal law enforcement. It is notable that our Founding Fathers anticipated this very conflict as evidenced by the discussion in the Federalist Papers. Their concern regarding unrestrained government resulted in the separation of powers, checks and balances, and ultimately, the Bill of Rights. Where these important objectives merge, it is critical that we, as a democratic Nation, pay close attention to traditional Fourth Amendment principles. The Fourth Amendment has served this Nation well for 220 years, through many other perils. ...

Moreover, the constitutionally required interplay between Executive action, Judicial decision, and Congressional enactment, has been eliminated by the FISA amendments. Prior to the amendments, the three branches of government operated with thoughtful and deliberate checks and balances - a principle upon which our Nation was founded. These constitutional checks and balances effectively curtail overzealous executive, legislative, or judicial activity regardless of the catalyst for overzealousness. The Constitution contains bedrock principles that the framers believed essential. Those principles should not
be easily altered by the expediencies of the moment.

Score one for the Fourth Amendment.