Clinton, who is visiting the African country for the first time since Islamist President Mohammed Morsi was elected, was also taunted with Monica chants by a crowd of demonstrators. The chants referred to Monica Lewinsky, a White House intern with whom Clinton's husband, then-President Bill Clinton, admitted to having an improper relationship in the 1990s.
Egyptian security officials also said some protesters chanted, Leave Clinton.
Protesters threw shoes and water bottles, as well as tomatoes. Although neither Clinton nor her vehicle were hit by anything, an Egyptian official was struck in the face by the red fruit.
The political affiliation of the demonstrators wasn't clear. However, Reuters reported that anti-Islamist protesters were yelling outside Clinton's hotel during her trip, accusing the U.S. of helping the Muslim Brotherhood rise to power.
The demonstrators weren't the only ones critical of Clinton and the U.S., though, as the secretary of state was snubbed by prominent Egyptian Christians on Sunday, according to MSNBC. Christian businessmen, clerics, and politicians were absent from a scheduled meeting with Clinton because of their expressed feeling that the U.S. has favored Muslims over Christians in Egypt since the revolution that deposed former President Hosni Mubarak last year.
Estimates of Egyptians' religious affiliations vary, between 80 percent and 90 percent on the Muslim side and from 10 percent to 20 percent on the Christian side.
A Clinton representative said the secretary of state had hoped to use the meeting on Sunday to smooth things over with the Christians and reassure them they are not being ignored.