Civilian injuries and death are regrettable and tragic and throughout its operations in Gaza, Israel took serious measure to avoid harming civilians. Israel targeted Hamas operational centers, most of which were deliberately located in densely populated areas. Hamas cynically and deliberately put ordinary Palestinians in harm's way by establishing its terrorist infrastructure – manufacturing, storage, training and strategic planning – within densely populated areas, in the midst of homes, schools, mosques and hospitals. Israel enacted procedures to warn civilians though leafleting and phone calls, that their neighborhoods and buildings were located in the vicinity of military operations and urging them to leave the area.

Additionally, Hamas inserted itself within the civilian population of Gaza, fought in civilian clothing, making it all the more difficult to distinguish between civilians and terrorist. According the Israeli military intelligence officials, Hamas stashed weapons in houses, schoolyards, mosques and Hamas leadership bunkered beneath a major Gaza hospital.

The Israeli military launched an investigation into the January 6 shelling of a school run by the United Nations Relief and Works Agency for Palestinian refugees (UNRWA) which tragically killed civilians. Israel said that preliminary information indicated that Hamas operatives had launched a mortar attack on Israeli soldiers. Israel responded to the attack. Palestinians living near the school told international news agencies that Hamas operatives were seen at the school right before the attack and called on nearby residents to pile sand around the school compound.

On February 3, 2009, UNRWA announced that the forty-three Palestinians killed were outside of the school.  No shells hit the school building.  The IDF had stated following the incident that mortars had been launched from outside the school compound and that they responded to that attack.