One boy died Thursday, and the other died a day earlier, said Adel Muhsin, the Health Ministry's inspector-general. Six other children at the orphanage have been diagnosed with cholera, he said.
The al-Hanan orphanage became infamous last June, when U.S. and Iraqi soldiers found 24 severely malnourished boys there in a dark room, some tied to beds and too weak to stand once they were unbound. Afterward, Iraqi officials said the boys were transferred to a different building and were being properly cared for.
Muhsin blamed this week's cholera deaths on unclean water being stored in a tank on the facility's roof.
"The people in the orphanage did not clean the water tank, and they kept filling it with water while neglecting our health experts' recommendations," Muhsin told The Associated Press. "The percentage of the chlorine in the tank was zero when we inspected it."
Arrest warrants were issued in June for three employees of the orphanage, but they have gone into hiding and remain at large.
The World Health Organization has confirmed more than 3,300 cholera cases in Iraq and at least 14 deaths from the acute and rapid dehydration it causes.
The outbreak first detected Aug. 14 in Kirkuk in northern Iraq has now spread to half of the country's 18 provinces.
Cholera is a gastrointestinal disease that is typically spread by drinking contaminated water and can cause severe diarrhea that, in extreme cases, can lead to fatal dehydration. It can be prevented by treating drinking water with chlorine and improving hygiene conditions.
The global health body estimates that more than 30,000 people in Iraq have come down with acute watery diarrhea, which may later be confirmed as cholera.
The hardest-hit provinces are Kirkuk with 2,309 cases and Sulaimaniyah with 870 - both in northern Iraq.