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Mr Borrell sought to express solidarity with Israel on his first visit to the country since the October 7 attacks, and voice international concern about Palestinian civilian casualties as Israeli forces seek to destroy Hamas in Gaza.
The EU's 27 member countries have deeply rooted differences about the wider Palestinian-Israeli conflict and Mr Borrell faced a difficult task as he tried to find middle ground.
After visiting the devastated Kibbutz Be'eri, a major target of the October 7 assault, with Israeli Foreign Minister Eli Cohen, Mr Borrell drew on his own experience of living and working in a kibbutz in the 1960s.
"I know what a kibbutz means for the Israelis," he said, after walking among destroyed homes and a kindergarten in the settlement near the border with Gaza, wearing a flak jacket with the EU flag.
After the kindergarten visit, Mr Borrell carried a small red Lego brick in one hand.
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Hamas killed about 130 residents of the kibbutz and kidnapped others, according to Israeli officials.
"I understand what the family of the Kibbutzims feel when their sons, or their fathers or daughters are kidnapped," said Mr Borrell, a veteran Spanish Socialist politician.
But he also called on Israel to heed international calls to do more to help and protect civilians in Gaza.
"I understand your rage but let me ask you not to be consumed by rage," Mr Borrell said.
"Not far from here is Gaza. One horror does not justify another."
Israel insists it is trying hard to prevent civilian casualties in Gaza but has no choice but to fight in civilian areas because that is where Hamas operates.
Mr Cohen said Hamas was to blame for the October 7 attacks and for the current plight of Palestinians in Gaza.
"There is only one responsible for this atrocity, for the massacre of the 7th of October, for the world that started after and also the suffering of the people in Gaza – it's Hamas, which is sponsored by Iran," he said.
Mr Borrell also met relatives of people taken hostage by Hamas. They made emotional pleas for the EU to help secure the release of their loved ones.
Mr Borrell pledged to raise the issue in a meeting this weekend with the Emir of Qatar, Sheikh Tamim, whose country has been heavily involved in trying to reach a deal to free at least some of the hostages.