Speaking prior to this month's 40th anniversary of the Stonewall riots, Clinton said: "The example set by those fighting for equal rights in the United States gives hope to men and women around the world who yearn for a better future for themselves and their loved ones.
"The persecution of gays and lesbians is a violation of human rights and an affront to human decency, and it must end.
"As secretary of state, I will advance a comprehensive human rights agenda that includes the elimination of violence and discrimination against people based on sexual orientation or gender identity."
Seven countries punish homosexuality with execution. They are Iran, Mauritania, Nigeria, Saudi Arabia, Sudan, the United Arab Emirates and Yemen.
Last week, it was announced that gay partners of US diplomats stationed overseas are to receive equal benefits in plans unveiled by Clinton.
Howard Berman, head of the House Foreign Affairs Committee, had asked the State Committee to ensure benefits such as medical care, transport between postings and security training were offered to same-sex partners.
In a hearing on funding for the Foreign Service, he said: "It is my expectation, based on very recent conversations, that the secretary of state will move forward with implementing all of the benefits provided in that provision in the very near future."