In 2011, the state department's annual human rights report cited ally Saudi Arabia's abuses against gays. The country bans homosexuality outright.
Afghanistan also prohibits homosexual activity, and the same report found that authorities "sporadically" enforced the prohibition.
In the US, Republican presidential candidates criticised the administration's decision, with Texas Governor Rick Perry saying in a statement that "promoting special rights for gays in foreign countries is not in America's interests and not worth a dime of taxpayers' money".
Mrs Clinton acknowledged the US had its own mixed record on gay rights. As late as 2003, some states had laws that made gay sex a crime.
Earlier this year President Barack Obama signed into law a bill repealing the "Don't Ask Don't Tell" law and allowing homosexuals to serve openly in the US military.
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