After the 1986 reorganization of the military undertaken by the Goldwater-Nichols Act, the Joint Chiefs of Staff do not have operational command of U.S. military forces. Responsibility for conducting military operations goes from the President to the Secretary of Defense directly to the heads of the Unified Combatant Commands and thus bypasses the Joint Chiefs of Staff completely.

Today, their primary responsibility is to ensure the personnel readiness, policy, planning and training of their respective military services for the combatant commanders to utilize. The Joint Chiefs of Staff also act in an advisory military capacity for the President of the United States and the Secretary of Defense. In addition, the Chairman of the Joint Chiefs of Staff acts as the chief military advisor to the President and the Secretary of Defense. In this strictly advisory role, the Joint Chiefs constitute the second-highest deliberatory body for military policy, after the National Security Council, which includes the President and other officials besides the Chairman of the Joint Chiefs.

http://en.wikipedia.org/wiki/Joint_Chiefs_of_Staff