Data from 1,849 households that contained 12,801 individuals in 47 clusters was gathered. 1,474 births and 629 deaths were reported during the observation period. Pre-invasion mortality rates were 5.5 per 1000 people per year (95\% CI 4.3–7.1), compared with 13.3 per 1000 people per year (10.9–16.1) in the 40 months post-invasion. We estimate that as of July, 2006, there have been 654,965 (392,979–942,636) excess Iraqi deaths as a consequence of the war, which corresponds to 2.5\% of the population in the study area. Of post-invasion deaths, 601,027 (426,369–793,663) were due to violence, the most common cause being gunfire.
Author Mark Goldblatt notes in an article on National Review that, in these calculations, one should also consider the fact that, before the invasion, Iraq was subject to sanctions that were lifted after the American occupation. By some estimates, the sanctions were causing about 150,000 deaths a year. This means that, since 2003, about 450,000 deaths might have been avoided because of the end of the sanctions.
Considering that one would have expected 450,000 fewer deaths, and one gets instead 650,000 more, the conclusion would be that the extra deaths caused by the occupation would be in excess of a million. Of course, simply adding the two numbers is problematic for a few reasons: some of the effects of the sanctions (for example, on the health care system) may be similar to the effects of the occupation, and hence would be having similar (rather than nearly disjoint) effects. Most importantly, it has been alleged that the estimates on deaths caused by the sanctions were overstated.
Anyways, what is Goldblatt approach? He subtracts one number from the other! You know how this works: I owe you \$20 dollars, now lend me another \$30 and I will give you the \$10 difference tomorrow. If I may suggest an improvement to his methodology, he should also subtract the number of deaths that occurred in Switzerland over the same period of time. I am sure he would get even more accurate estimate.
Update: see also Tim Lambert at scienceblogs.