Medical doctors leaving less developed countries are now part of a global labour market. This doctor migration has been extensively studied from economic and health systems perspectives. Seldom, however has the specific role of the conflict or the collapsing state been considered as a cause of migration. Using hospital staffing records we measured the changes in numbers of medical specialists at 12 Iraqi tertiary hospitals (in Baghdad, Basra, Erbil and Mosul) between 2004 and 2007. For doctors leaving their posts, we attempted to determine destinations and circumstances of departure. We counted 1243 specialists in the 12 hospitals on January 1, 2004. This declined to 1166 or 94% of the original number by late 2007. In Baghdad, specialists decreased to 78% by late 2007, Outside Baghdad, specialists numbered 134% of the original count by 2007. In Baghdad, replacements kept pace with losses until 2005, with loss rates peaking in 2006 at 29%. Outside Baghdad, gains exceeded losses each year. Violent event rates associated with the migration of doctors were estimated as: threats 30/1000 doctors; kidnappings 6.7/1000; violent deaths 16.5/1000, and any violent event 36.7/1000. Specialists who left Baghdad were 2.5 times more likely to experience a violent event than doctors elsewhere. Specialists departing teaching hospitals were 2.3 times more likely to experience a violent event than those in general hospitals. Of specialists leaving hospital posts for which data were available, 39% went elsewhere in Iraq and 61% left the country. These findings suggest a major loss of human capital from Iraq's hospital sector, a loss that is likely to require some years to fully replace.