Only days after taking the helm as defence secretary, Carter paid an unannounced visit to a country where US troops have been deployed for more than 13 years but are now in a scaled back role.
"The reason for this destination, Afghanistan, in my very first week in office as the secretary of defence is because this is still where we have 10,000 American troops. They come first in my mind, always," Carter told reporters aboard his plane before landing in the Afghan capital.
Carter's visit comes as President Barack Obama faces a decision about the timetable for a troop drawdown in Afghanistan. Under the current plan, the 10,000-strong force is due to drop to roughly 5,000 by the end of 2015 and then pull out altogether by the time Obama leaves office in two years.
But the Obama administration has already adjusted the pace of the withdrawal, allowing 1,000 additional American forces to remain this year.
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In testimony before senators this month before he was sworn in at the Pentagon, Carter signalled he was open to revising the troop withdrawal schedule if necessary.
Afghan leaders and some lawmakers have urged Obama to reconsider the withdrawal timetable, warning that an early US exit could jeopardise security and discourage international aid.
Carter was due to hold talks with the US commander in Kabul, Campbell, as well as General Lloyd Austin, head of US Central Command which oversees American forces in the Middle East and Central Asia, who travelled to Kabul to take part in the talks.
Asked about the presence of the Islamic State group in Afghanistan, Carter played down the threat, saying some Taliban insurgents were making an attempt at "rebranding" themselves.