The latest International Religious Freedom Report exposed several violations, including the rise of anti-semitism in nations from Venezuela to the Netherlands and an openly anti-semitic political party in Hungary.
Suzan Johnson Cook, America's Ambassador for International Religious Freedom, said nearly half of the world's countries have governments that either abuse religious minorities or refuse to intervene in cases of abuse.
"In Egypt, the former regime routinely discriminated against minorities, particularly coptic Christians," Cook said.
Speaking before members of the Carnegie Endowment for International Peace Monday, Secretary of State Hillary Clinton said the jury was still out on whether Egypt's Islamist political parties will equally represent non-Muslims.
She added that the Obama administration's future relationship with President Mohammed Morsi and the Muslim Brotherhood would depend on how they respect the rights of Coptic Christians, women and other minorities.
"They wonder, will a government looking explicitly to greater reliance on Islamic principles stand up for non-Muslims and Muslims equally? Since this is the first time that Egypt has been in this situation, it's a fair question," Clinton said.
She did commend Egypt's new president for saying "clearly and repeatedly, in public and private, that he intends to be the president of all Egyptians."
"We are going to judge by actions, not words, and the actions are just at the very beginning stages," Clinton added.
Monday's religious freedom report also criticized U.S. allies Afghanistan and Pakistan, while taking aim at chronic violators Iran, China, and North Korea as well.
The report highlighted blasphemy and religious "defamation" laws in Muslim countries.