Clinton said the United States was well aware Iran had stepped up its diplomatic activities in the region, citing Venezuela and Bolivia in particular.
"We can only say that is a really bad idea for the countries involved," Clinton told a State Department briefing on Latin American relations.
"This is the major supporter, promoter and exporter of terrorism in the world today," she said. "If people want to flirt with Iran, they should take a look at what the consequences might well be for them. And we hope that they will think twice."
Clinton said Washington would continue to express concerns about Venezuela - where Chavez won a referendum in February that allows him to keep running for re-election - and about Nicaragua, where the Supreme Court in October opened the way for leftist President Daniel Ortega to seek a new term in a 2011 election.
"We all hope in the not too distant future to be able to see a democratic Cuba...something that would be extraordinarily positive for our hemisphere,"