Tuesday's visit was initially slated for last month, but Netanyahu rescheduled it when Israeli commandos boarded a Turkish ship that was attempting to break Israeli's marine blockade of Gaza and resulted in a skirmish and nine casualties.
The United States sided with Israel on the issue, which helped ease tensions that began in March when Israel announced the building of 1,600 new Jewish housing units in the West Bank.
The Obama administration views the settlements as an obstacle to the peace process during his visit to Jerusalem.
In response to the announcement of the housing units, the Obama administration publicly upbraided Israeli Prime Minister Benjamin Netanyahu and later gave him a chilly reception at the White House.
While the two allies share common goals and values, the relationship has at times been rocky.
In 1969-70, U.S. President Richard Nixon pressured Israel to accept a new cease-fire with Egypt along the Suez Canal and even slowed arms shipments to Israel.
In 1975, Secretary of State Henry Kissinger announced a "reassessment" of U.S. policy and again slowed aid to press Israeli Prime Minister Yitzhak Rabin's new government for a withdrawal from Egypt's Sinai Peninsula.
In 1982, President Ronald Reagan pressured Israel to stop bombarding Beirut, Lebanon and withdraw from most of that country, in part through public hints of changes in the relationship.
In 1996 and again in 1999, President Bill Clinton refused to see Israeli Prime Minister Benjamin Netanyahu and publicly hinted that Israelis should vote for Netanyahu's political rivals.
And President George W. Bush privately pressed Israel on some points, such as allowing Hamas to run in the Palestinian election in 2006, though without a public crisis.