A tomato struck an Egyptian official in the face, and shoes and a water bottle landed near the armoured cars carrying Clinton's delegation in the port city of Alexandria.
A senior state department official said that neither Clinton nor her vehicle, which were around the corner from the incident, were struck by any of the projectiles.
Protesters chanted: "Monica, Monica", a reference to Former President Bill Clinton's extra-marital affair. Some chanted: "leave, Clinton", Egyptian security officials said.
It was not clear who the protesters were or what political affiliations they had. Protesters outside Clinton's hotel on Saturday night chanted anti-Islamist slogans, accusing the United States of backing the Muslim Brotherhood's rise to power.