Since 2004, there have been a number of studies (seriously, click that link even if it's just going to be summarized for you here) that have provided estimates on the number of Iraqis who have been killed during the ten year war. In October 2004, the Lancet published findings from household surveys conducted by local Iraqi medical personnel and the John Hopkins School of Public Health. it was estimated that within the first eighteen months of the war, there had been "excess deaths" of 98,000.
In a 2006 survey by John Hopkins, published in the Lancet, it was found that the total number of dead Iraqis - fighters and civilians - was at 650,000. The Iraqi Ministry of Health also conducted a survey at the same time as JH (using the same method of house-hold surveys) found excess deaths of 400,000. Of these near half-million deaths, 151,000 were by the violence. According to the report, "[overall] mortality from nonviolent causes was about 60% higher in the post-invasion period than in the pre-invasion period. "
That was from 2002-2006.
The most recent study was published in October 2013. A collaborative effort between John Hopkins, Simon Fraser, Washington and Mustansiriya universities, the survey explores the numbers from 2003 to 2011 and suggests that the 'excess deaths' in the Iraq war can be estimated at 461,000.
From the report's Abstract's conclusion (emphasis added):
"Beyond expected rates, most mortality increases in Iraq can be attributed to direct violence, but about a third are attributable to indirect causes (such as from failures of health, sanitation, transportation, communication, and other systems). Approximately a half million deaths in Iraq could be attributable to the war."