Labelled by the Iraqi government and the US forces as simply terrorists, the militias are actually a diverse collection of groups holding very different views about the country's future - yet all share the same commitment to driving US-led troops out of Iraq.
At its core the insurgency stems from the Sunni heartland at the centre of the country where Sunni Iraqis feel alienated by the presence of US troops and their lack of power in the Shia-dominated elected government.
Former members of Saddam Hussein's Baath party form the largest single section, with Islamists, tribal groups, local militias and foreign fighters all heavily involved.
The militias have also formed alliances with criminal gangs in towns such as Samarra.
Thousands of Iraqis have been
killed in militia bombings
The Baathists themsleves have since split into at least two factions - those who remain loyal to Saddam and others who have broken away from the former Iraqi leader.
Al-Qaida in Iraq - led by Abu Musab al-Zarqawi, a Jordanian-born radical - has the highest profile but is believed to number 3,000 at most, although members carry out many of the bloodiest and headline-grabbing attacks.
Shia militant groups that clashed with US forces in the past, most notably the al-Mahdi Army, led by Muqtada al-Sadr, a cleric, have opted to join the political process and have formed political parties.
Many members of the militias are thought to be embittered soldiers from the former Iraqi army - disbanded by the US in May 2003 - who have used their military expertise and access to weapons against US-led forces.
Zaki Chebab, author of Iraq Ablaze: Inside the Insurgency, says this has been key to their effectiveness.
"The knowledge of government buildings and the positioning of mortars point to a high degree of military training"
"You can't give a 21-year-old jihadist a gun and expect him to carry out attacks of this level. The knowledge of government buildings and the positioning of mortars point to a high degree of military training."
The militias also draw widespread support from the Sunni communities in which they operate.
Liqa Maki, an analyst for Aljazeera, said: "They are the sons, husbands and brothers of the people there, so obviously they are supported.
"People fight because there is an occupation. Outside Baghdad, the rebels rule and when US soldiers come to their houses, kick down their doors and arrest their wives - they feel this is a big insult and want to take revenge - this is the soul of the resistance."
Despite this no Sunni group has openly attempted to translate its military activities into popular or political support.
As Dr Saad Jawad, lecturer in political science at Baghdad University, says: "The Baathists need to do more to show that they have moved on from the Saddam era and apologise for the mistakes of the past, and the Islamists will never be popular in a country with the secular traditions of Iraq."
There have also been high numbers of Iraqi civilian casualties caused by the tactics of the militias, particularly suicide bombings in crowded public places.
Human rights groups have
labelled attacks as war crimes
Such indiscriminate attacks on civilians have led human rights groups to accuse some militias of commiting war crimes.
At the same time, while the conflict in Iraq has always been an international problem, it has now spread to involve other countries in the region.
Last November al-Qaida in Iraq claimed responsibility for the bombing of three hotels in Amman, Jordan, killing 57 people.
It has also threatened to attack Israel, although to date that remains merely a threat.
Meanwhile, the US has accused Syria of allowing foreign jihadists to cross its border into Iraq.
Iran also has been linked with attacks on British troops by Shia militias based in the south of the country, although it, like Syria, denies any involvement with Iraqi militias.
Chehab believes that Afghan groups have begun using tactics inspired by Iraqi militias in their own resurgent military campaign, such as the use of suicide bombings.
As for the future of shape of the militia campaign, the bombing of the Shia Askariya shrine in Samarra last month could prove to be a turning point.
Chehab believes that the Samarra bombing was carried out by al-Qaida in Iraq in an attempt to force the militias into open civil war before recent talks between US forces and some militia representatives came to fruition.
Any truce between US forces and the more moderate militias could isolate al-Zarqawi and leave him vulnerable, Chehab believes.
Negotiations such as these are the key to ending the continuing violence in Iraq, he thinks.
For Maki, the future in the country looks bleak, with the country teetering on the edge of an all-out sectarian conflict.
"The resistance faces a difficult choice – do they keep fighting American troops or do they fight a civil war?" he says.
"At the moment Iraq is very weak - one bombing could lead to civil war, Iran could spark a civil war, Syria could spark a civil war, the resistance could spark a civil war - it is a dangerous situation."