Several hundred protesters - relatively few by recent Egyptian standards - chanted anti-U.S. and anti-Islamist slogans outside Clinton's hotel on Saturday night. Some said the United States had backed the Brotherhood's rise to power.
In her meetings with civil society groups, notably members of Christian communities, Clinton sought to dispel the idea.
"She wanted, in very, very clear terms, particularly with the Christian group this morning, to dispel that notion and to make clear that only Egyptians can choose their leaders that we have not supported any candidate, any party, and we will not," a senior U.S. official told reporters.
Clinton was due to travel then to Alexandria for a flag raising ceremony at a reopened U.S. Consulate in the Mediterranean port city and then to Jerusalem for talks on Israeli-Palestinian peace before returning to Washington.