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Traffic was at a standstill and Israelis stopped in the streets to show tribute on what is called Holocaust Martyrs' and Heroes' Day on Thursday morning.
The silent mourning of the dead was followed by the laying of wreaths at the Yad Vashem Holocaust memorial in Jerusalem by President Ezer Weizman and other leaders of the Jewish state.
As the tones of the wailing siren died away, Israel prepared for a day-long recitation of the names of those who died, spoken by their family members and friends.
During the 24-hour commemoration, businesses, restaurants and theatres are closed.
On Wednesday, Israel's leaders attended a sunset ceremony, also at Jerusalem's Yad Vashem Holocaust museum, to mark the start of Holocaust Remembrance Day and acknowledge the suffering of the six million victims.
According to Israel's Holocaust museum, those already in Israel were often "uninterested in the survivors' stories and their emotional burdens, and most of the new arrivals enclosed themselves within a wall of silence."
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The Israeli President, Ezer Weizman, spoke of the triumphs and tragedies of the Jewish nation in the past 50 years.
"In this century, the Jewish people reached one of its lowest points during the Holocaust. However, it also attained one of its most impressive achievements - the establishment of the state of Israel as a national homeland for the Jews.
"Another accomplishment is the revival of the Hebrew language, which was not forgotten even after 2,000 years."
He also expressed optimism about the peace process, saying he believed a comprehensive peace would come in a short time.
The Israeli Prime Minister, Binyamin Netanyahu, is spending the memorial day in Poland, to participate in the annual 'March of the Living' from the former Auschwitz-Birkenau death camp, where German invaders murdered up to 1.5m people, the vast majority Jews from across Europe.
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