The Central Intelligence Agency, which until recently operated outside the military establishment, is expected to stay on in various guises within the 17,000 U.S. personnel who will remain under State Department jurisdiction.
The CIA has become increasingly militarized since the Sept. 11, 2001, terror attacks, and most of its establishment -- including a heavily enlarged paramilitary division -- is engaged in the counter-terrorism battle to one degree or another.
And with Gen. David Petraeus, the former military commander in Iraq and Afghanistan who wrote the army's counter-insurgency manual, now the director of the CIA, the agency can be expected to maintain some covert operations.
Even so, the loss of clandestine facilities means "there will be a considerable lapse in and degradation of the U.S. intelligence-gathering and situational awareness capabilities in Iraq," observed U.S.-based global intelligence consultancy Stratfor.
One of the major drawbacks to the military withdrawal is that Iraq's intelligence and security services, heavily infiltrated by Shiite groups with strong links to Iran, are not likely to be capable of waging an effective and non-sectarian counter-terrorism campaign.
U.S. military intelligence and Special Forces ran operations against Iran and its proxies in Iraq, and even into Syria, Iraq's northern neighbor and Tehran's key ally, intelligence sources say.
With tension escalating between the Islamic Republic and the United States, not to mention Israel, the closures could impede such operations.
Iran's influence in Iraq is expected to swell as U.S. power departs, compounding the loss of these intelligence bases around the country.
Iran has an extensive and deeply entrenched clandestine network across the entire Gulf region, and with the U.S. withdrawal from Iraq the way will be more open to expand that network across Iraq, into Syria and Lebanon, right up to Israel's doorstep.
Without the intelligence bases in Iraq, American efforts to prevent Iran filling the power vacuum in Iraq will be seriously weakened.
"The problem is Iran's military power in Iraq is primarily covert and unconventional, including both proxies and militias composed of Iraqis and clandestine operatives that can effectively move into and around Iraq with considerable freedom," Stratfor noted.
One possibility to limit the damage is building a wider counter-terrorism apparatus in Turkey, Iraq's northern neighbor, a growing power in the region and a longtime NATO ally.
But that could come with a hefty political price tag.
Turkey has been pressing U.S. President Barack Obama's administration since June to provide it with MQ-1 Predator unmanned aerial vehicles to monitor separatist rebels of the Kurdistan Workers Party, known as the PKK, it is fighting in southern Anatolia and their havens in Iraq's Kurdish enclave.
Turkey's need for UAVs has heightened amid reports Heron surveillance craft acquired from Israel before the two allies broke up in 2010 are currently undergoing maintenance in Israel.
To counter this, the Americans plan to redeploy some Predators, which they used as missile-armed killer-hunters in Iraq, to the big U.S. air base at Incirlik in southern Turkey for anti-PKK operations.
The Turks have been heavily dependent on U.S. intelligence on PKK movements.
But using U.S. drones based in Turkey could drag the Americans into yet another seemingly intractable Middle Eastern conflict just as they're extricating themselves from a disastrous nine-year occupation in Iraq.
Classified diplomatic cables released by WikiLeaks reveal Turkey has persistently pressed Washington to step up its involvement against the PKK before the U.S. pullout wraps up Dec. 31.
Turkish Prime Minister Recep Tayyip Erdogan said Sept. 24 the Americans have agreed "in principle" to station the Predators in Turkey as the 27-year-old war against the PKK escalates.
There have been some strains between Washington and Ankara in recent years, but several weeks ago the Turks agreed to station U.S. advanced radar units in their country to monitor ballistic missile launches in Iran.
U.S. cooperation with Erdogan on intelligence and security issues was given impetus after the joint Turkish-U.S. Kurdistan intelligence center in Erbil, capital of the semiautonomous Kurdish enclave in northern Iraq, closed in October.
Soon after, PKK guerrillas mounted near-simultaneous attacks on eight military targets in southeastern Turkey, killing 26 Turkish soldiers Oct. 19.