The Federal Criminal Court was established in Bellinzona on 1 April 2004. It is comprised of three chambers: the Criminal Chamber and two Appeals Chambers.

The Criminal Chamber rules in the first instance for criminal offences expressly falling under federal jurisdiction under Articles 23 and 24 of the Criminal Procedure Code (CrimPC, SR 312). These federal criminal offences constitute an exception to the primary jurisdiction of the cantons in matters of criminal prosecution. They relate, in particular, to crimes and offences against federal interests (those committed by or against federal employees, federal institutions or persons protected under international law, corruption, etc.), offences involving explosives, economic crime, organised crime and cases of money laundering that are international or inter-cantonal in scope.

The Criminal Chamber also deals with offences contravening various federal acts, such as the Civil Aviation Act (CAA, SR 748.0), the Atomic Energy Act (AtA, now repealed), the Financial Market Infrastructure Act (FinMIA, SR 958.1) and the War Material Act (WMA, SR 514.51). Other areas covered include the foreign transfer of immaterial goods and know-how relating to war material.

The Lower Appeals Chamber hears federal criminal appeals against procedural decisions and actions by the Federal Criminal Police and the Office of the Attorney General of Switzerland (OAG), as well as against decisions taken by the coercive measures courts, which issue detention orders. The Lower Appeals Chamber also hears appeals against decisions and rulings of the Criminal Chamber that are not classed as judgments. In addition, it deals with appeals and complaints referred to it under administrative criminal law as well as conflicts of jurisdiction between different cantons or between cantons and the Confederation. Finally, the Lower Appeals Chamber has the power to hear appeals on international mutual assistance in criminal matters, with decisions mainly relating to the extradition of suspects or convicted persons, assistance given in the context of foreign criminal proceedings, the delegation of criminal proceedings and the enforcement of judgments including foreign judgments.

As the second instance in federal criminal cases, the Higher Appeals Chamber hears appeals against Criminal Chamber judgments that wholly or partially conclude proceedings. It also hears applications for a review of Criminal Chamber or Higher Appeals Chamber judgments that have come into effect as well as appeals against summary penalty orders issued by the Office of the Attorney General of Switzerland (OAG), subsequent court decisions and decisions rendered in independently conducted action procedures.