The removal of 20 posts along the heavily-fortified frontier was one of the steps agreed at a September summit between the South's President Moon Jae-in and the North's leader Kim Jong Un in Pyongyang, part of a rapid reconciliation drive on the peninsula.
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In November, North Korea blew up the 10 facilities while the South tore down 10 on its own side using excavators.
Seoul's defence ministry said early on Wednesday that South Korean inspectors will visit each of the guard posts on the North's side to verify their dismantlement and to ensure that all firearms and troops have been removed.
North Korean inspectors will carry out the same process at the South's bunkers, it added.
"This marks the first time since the division that the soldiers of the North and South ... are peacefully crossing the military demarcation line," the ministry said in a statement.
The dovish Moon has pursued a policy of engagement with its isolated, nuclear-armed neighbour, in increasing contrast to Washington, which insists pressure should be maintained on Pyongyang until it denuclearises.
Despite its name, the area around the Demilitarised Zone (DMZ) is one of the most fortified places on earth, replete with minefields and barbed-wire fences.
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But under plans to ease tensions agreed in Pyongyang, the two Koreas have demilitarised the border truce village of Panmunjom, leaving it manned by 35 unarmed personnel from each side.
Officially called the Joint Security Area (JSA), the enclave is the only spot along the 250-kilometre (155-mile) frontier where soldiers from the two Koreas and the US-led UN Command stand face to face.
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