The relationship between ISI and some terror groups remained a concern for the US, even though there has been a remarkable improvement in cooperation from the ISI in last nine months, Clinton told reporters travelling with her.
"... we are constantly assessing that (relationship between ISI and terrorist organisations) and because it remains a concern to us," she said in response to a question.
Clinton said the US continues to raise several issues with Pakistan, with the Mumbai trial prominent among them.
"We are clearly pushing for the trials of the Mumbai attackers and planners to go forward," she said.
"We are very much focused on them, because we see them as a threat to Pakistan, we see them as a threat to India, we see them as a threat to stability in the region. We don't think its good for anybody," she said.
Clinton said "No" when asked: "Are you convinced that there is no more collaboration between the military and the ISI in assisting certain terrorist groups like Lashkar e-Tayyiba?" and added: "No, but I'm not unconvinced".
Clinton, however added that the level of cooperation from the Pakistani military and intelligence services "has increased geometrically in the last nine months".
She said she believed the two countries had made progress in creating a base of trust but "nine months is not a lot of time to turn around a relationship that has a lot of scars to it.
"... But I think it is fair to say that we have really increased the level of conversation and sharing of information over the last nine months that is unprecedented at least since we were in there working with them to create these organisations that are now the source of a lot of our problems," Clinton said.
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