Since the end of the IDF's operation in Gaza, there is a growing debate over Palestinian casualty claims. While the Palestinian Centre for Human Rights (PCHR) and the Palestinian Ministry of Health have announced that the majority of fatalities were civilians, the IDF has estimated that "more than two-thirds of [the deaths] were Hamas members." (The Jerusalem Post has reported that "IDF Military Intelligence has set up a team to produce a comprehensive list of Palestinian fatalities… It will be completed within two weeks, officials said, but it is not clear whether it will be made public." The International Herald Tribune claimed that "Israel … said it has the names of more than 700 Hamas militants killed in fighting.")

PCHR is a highly politicized NGO, a leader in the anti-Israel "lawfare" movement, and funded by the EU, Norway, Ireland, Sweden, and other European governments and organizations. On January 21, 2009, PCHR alleged that there had been a total of 1,285 Palestinian deaths, among which 895 were civilians – meaning almost 70% of were civilian. These figures were repeated by the Jerusalem Post, Ha'aretz, Reuters Alertnet, and others. PCHR's anti-Israel campaigning during war includes accusations of Israeli "war crimes," "crimes against humanity," "human holocaust," "collective punishment," "indiscriminate killing and continued systematic destruction of all the Palestinian institutions and civilian facilities in the Gaza Strip." PCHR, which consistently refers to Palestinian terrorism as "resistance," also has been preparing for new lawfare cases arising out of "Operation Cast Lead."

Al Mezan, another politicized Palestinian NGO, also claimed (January 15, 2009) that "about 70% of IOF's attacks casualties of these attacks are from families who were hit inside their homes or as they left their homes to flee these areas. Most of the other victims were also civilians." On January 14, 2009, Al Mezan claimed that only 13.9% of the deaths were "fighters."

PCHR's credibility has been questioned in a report by CAMERA: "PCHR includes in its civilian toll individuals identified by other sources as combatants and omits any mention of several slain senior fighters from terrorist groups. The omission of several publicized Hamas commanders should raise suspicion that other Hamas fighters have been omitted from its statistics." CAMERA also concluded that "[a]n analysis of the fatalities by age and gender shows that the majority of civilian fatalities recorded by PCHR are males between 15 and 50 years old, the same age profile as the combatants. This should raise concern that significant numbers of combatants may have been misclassified as civilians."

In addition to PCHR, the "authoritative" numbers published by the Palestinian Ministry of Health (PMOH) have been cited by journalists, diplomats, and humanitarian groups – including the UN and WHO, the International Red Cross and NGOs such as B'Tselem and Human Rights Watch. PMOH’s casualty statistics are accompanied by Palestinian propaganda, charging Israel with "genocide" and "massacres."

In a January 18, 2009 press conference, an unidentified senior IDF official stated, "the exact numbers are difficult to define, as Hamas intentionally conceals its losses in order to preserve its image of strength among Palestinian population." Similarly, the New York Times reported (January 10, 2009), "Hamas militants are fighting in civilian clothes; even the police have been ordered to take off their uniforms," making distinguishing combatants from civilians even more complicated.

Comparison of PCHR and the Ministry of Health figures:
  PCHR (21-1-09): Ministry of Health (18-1-09)
Total casualties 1,285 1,300
Total civilian casualties 895 “mostly civilians”
Total children casualties 280 410
Total women casualties 111 104
Total wounded 4,336 5,300
Total civilians wounded “mostly civilian” “mostly civilians”
Total children wounded 1,133 1,855
Total women wounded 735  795