Al Jazeera's James Bays, in Kabul, said: "There are a whole load of issues for these two presidents to discuss.
"They will be discussing regional issues - isues concerning Afghanistan, like the problem of opium in this country, the Taliban and its growth, particularly in the west on Iran's border."
He said that international issues will also be talked about following Gates's accusation of Iran is "double dealing" in Afghanistan by stating that they are a good neighbour to Kabul while on some level they aid the Taliban.
It is the first meeting between Karzai and Ahmadinejad since they were both reelected in disputed elections in 2009.
The US military invaded Afghanistan in 2001 to remove the Taliban, whom they accused of supporting al-Qaeda operatives, from power following the September 11, 2001, attacks on the USA of the same year.
Washington's forces remain in Afghanistan in an attempt to quell Taliban and al-Qadea attacks against Karzai's government.