A tomato struck an Egyptian official in the face, and shoes and a water bottle landed near the armored cars carrying Clinton's delegation in the port city of Alexandria after she gave a speech on democratic rights.
A senior U.S. official said neither Clinton nor her vehicle, which was around the corner from the incident, were hit by the projectiles, which were thrown as U.S. officials and reporters walked to the motorcade after her speech.
Protesters chanted "Monica, Monica," a reference to the extra-marital affair conducted by Clinton's husband, former President Bill Clinton, while in the White House. Others earlier chanted "leave, Clinton" an Egyptian security official said.
It was not clear who the protesters were or what were their political affiliations. Demonstrations have become common in Egypt since former President Hosni Mubarak, long-time U.S. ally, was brought down by mass street protests last year.
Egypt is gripped by political uncertainty as two major forces, the military and the Muslim Brotherhood, engage in a power struggle over the future of a country that remains without a permanent constitution, parliament or government.
On Saturday night, protesters outside Clinton's luxury hotel in Cairo chanted anti-Islamist slogans, accusing the United States of backing the Muslim Brotherhood's rise to power.
In her speech at the newly re-opened U.S. consulate in Alexandria, Clinton rejected suggestions that the United States, which had long supported former Mubarak, was backing one faction or another in Egypt following his ouster last year.
"I want to be clear that the United States is not in the business, in Egypt, of choosing winners and losers, even if we could, which of course we cannot," Clinton said.
"We are prepared to work with you as you chart your course, as you establish your democracy," she added. "We want to stand for principles, for values, not for people or for parties."