Turkey, a Nato member and a Muslim-majority nation, has been a site for anti-Americanism following the US-led invasion of Iraq in 2003.
Middle East peace
The Turkish prime minister, president and foreign minister will hold meetings with Clinton, who will also appear on a popular television chat show, hosted by four women, to offer the US's conciliatory message to Turkish people.
"I think Turkey will be an important, and can be an important, actor in implementing both security and peace policies in the region"
Ilter Turan, professor at Bilgi Istanbul University
Ankara's role in the Middle East peace process is believed to be top of Clinton's agenda during her one-day visit.
The US, it is believed, wants Turkey to mediate indirect talks between Syria and Israel.
Washington also wants Ankara to help convince its neighbours to allow their territory to be used as supply routes for US and Nato-forces battling the Taliban and al-Qaeda forces in Afghanistan.
Anita McNaught, Al Jazeera's correspondent in Istanbul, said that the agenda for the talks was extensive.
"This is a moment in history, certainly as the Turks would see it, where it seems like many roads, if not all roads to the resolution of the region's problems lead through Ankara," she said.
McNaught said that the Turkish government had been pro-active in dealing with Hamas and trying to bring the Israelis and Palestinians together in Middle Eastern peace talks.
She also said that Washington had asked Turkey to play a role in improving relations with Iran, and help with the situations in Iraq, Afghanistan and Georgia.
Ilter Turan, a professor at Bilgi Istanbul University, told Al Jazeera that Turkey's common past and religion with some of the countries of the region and an experience of dealing with populations of a similar nature could help.
"I think Turkey will be an important, and can be an important, actor in implementing both security and peace policies in the region," he said.
However, some people say that Turkey does not have the political will to increase their involvement in the myriad of areas desired by the US.
"They will face harsh opposition from the Islamist opposition, that they are killing their Muslim brothers, serving the western interests," Kadri Gursel, a columnist with the Millyet newspaper, told Al Jazeera.