The visit to Doha is part of a regional tour that has included stops in Saudi Arabia, Egypt and Israel. Mattis is scheduled to visit Djibouti tomorrow.
The Pentagon chief met with Emir Sheikh Tamim bin Hamad Al-Thani and was also due to hold talks with Defence Minister Khaled Al-Attiya during his brief visit to Qatar, which aims to improve ties with US President Donald Trump's administration.
Talks were expected to focus on the fight against the Islamic State group, the Syrian crisis, and the regional role of Iran, which Mattis has described as "destabilising".
Mattis, who commanded troops during the 2003 invasion of Iraq, said in Israel yesterday that there was "no doubt" Syria has kept some chemical weapons and warned President Bashar al-Assad's regime not to use them.
A small but strategic state in the Gulf, Qatar plays a key role in regional politics.
It is home to the Al-Udeid air base which houses around 10,000 US troops.
Rival Iran, an ally of Assad, played a crucial role in the evacuation deal, which according to sources in Baghdad included the release of a Qatari hunting party kidnapped in southern Iraq in 2015.
Washington has previously accused Doha of not doing enough to fight extremist organisations such as the Islamic State group. Qatar has denied the accusations.
The two countries have close economic ties, with national carrier Qatar Airways announcing in October the acquisition of up to 100 Boeing aircraft worth USD 18.6 billion (17.3 billion euros).
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