South Korea's defence ministry said initial discussions would focus on potential locations, as well as cost-sharing and a timeline for installation of the THAAD system.
The system fires anti-ballistic missiles into the sky to smash into enemy missiles either inside or outside the Earth's atmosphere during their final flight phase.
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Seoul and Washington announced their intention to begin formal talks on its deployment following Pyongyang's long- range rocket launch on February 7, which was widely regarded as a covert ballistic missile test.
The first official meeting has been on hold amid fierce opposition from China and Russia, with Beijing warning the deployment had the potential to "destroy" relations with Seoul.
China sees THAAD as a threat to the effectiveness of its own nuclear deterrent, arguing that it could be used to monitor Chinese missile launches as far inland as Xian in the northwest.
The defence ministry in Seoul stressed today that any deployment would be solely aimed at countering North Korea's "increasing nuclear and missile threats".
"North Korea has continued its nuclear tests and long-range missile provocations and defied South Korea and the international community's deterrence efforts," the ministry said.
China is South Korea's most important trade partner and, in deference to Beijing's sensitivities on the issue, South Korea had previously declined to formally discuss bringing in THAAD.
But North Korea's continued testing and Beijing's previous resistance to imposing harsh sanctions on Pyongyang triggered a change in Seoul's stance.
There is already a THAAD battery stationed in Guam, and Japan, the US's other key ally in the region, is also considering taking on the system.
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