Speaking at a joint news conference with Shimon Peres, Viktor Yushchenko said Ukraine valued its relationship with Israel and that the two states had a common past, as well as a common future.
"We regard Israel as our friend and partner in both regional and global issues," the press office quoted Yushchenko as saying.
Earlier on Wednesday, Yushchenko, in the country for a three-day visit, handed over to Israel declassified data on members of Ukraine's Jewish community arrested by the Bolsheviks between 1920-1940, as well as those executed in Soviet prisons in the post-WWII years.
Also some 100,000 people, mostly Jews, were massacred by Nazis in Babi Yar, a ravine on the northern edge of Kiev, in 1941-1943.
During talks with Peres, Yushchenko welcomed visa-free travel between Ukraine and Israel. Tel Aviv has sought to scrap visas for some former Soviet states, including Russia and Ukraine, saying that visa-free regimes should be reciprocal.
On Thursday, the Ukrainian leader is expected to meet with Israeli politicians and business people. Yushchenko is also set to hold talks with Palestinian leaders in Ramallah on the West Bank.