In 1995 Emergency refurbished and reopened a small hospital in the village of Choman, on the border with Iran, providing equipment and medical personnel specialized in war surgery. The healthcare situation in Iraq was critical: medical equipment, medical supplies and specialized personnel were all lacking, due in part to the heavy embargo imposed on Iraq after the first Gulf War.

In 1996 Emergency opened the first Surgical Centre for war victims in Sulaimaniya, the second largest city in Iraqi Kurdistan.
The Centre was the very first hospital in this area to provide free specialist treatment for firearm, bomb and landmine injuries, as well as a thorough rehabilitation program. Over the years Emergency's work has diversified to include rehabilitation for spinal patients, emergency and elective optical surgery and treatment of burn patients. In 1997 Emergency created a specific unit for paediatric burn patients; in 2003 a unit for adult burn patients.

In 1998 Emergency built a second Surgical Centre in Erbil to provide surgical and medical care to a part of the population that was out of reach to Emergency's ambulances due to disastrous road conditions and the ongoing conflict at that time between the two main Kurdish factions. Erbil was in the area under Kurdistan Democratic Party (KDP) control; Sulaimaniya was ruled by the opposing Patriot Union of Kurdistan (PUK). The Surgical Centre in Erbil was later enlarged: in the year 2000 a unit for paediatric burn patients was opened, in 2002 a unit for spinal patients and in 2003 a unit for adult burn patients.

In early 2004, having ascertained that the local staff would be able to work independently and that Kurdish authorities had adequate financial resources, Emergency began transferring the Surgical Centres to regional health authorities. The handover was completed on April 30th, 2005: these facilities are now an integral part of the national health system and continue to provide free of charge high quality assistance.