The two discussed issues ranging from Afghanistan and Pakistan to counter-terrorism and women's empowerment.
The talks were held days after the US exempted India from sanctions in return for cutting imports of Iranian oil.
After Wednesday's talks, Mrs Clinton spoke about a "closer convergence" of strategic interests between the US and India.
She welcomed the progress made in the US efforts to invest in India's civilian nuclear industry.
Trade has grown from $9bn in 1995 to $100bn this year.
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