The audit, which will take at least three weeks, was agreed by the two rival candidates Abdullah Abdullah and Ashraf Ghani at the weekend following two days of frantic diplomacy by US secretary of state John Kerry.
"The auditing will officially begin on Thursday, it will be done in Kabul and in commission's headquarters," Noor Mohammad Noor, spokesman for the Independent Election Commission (IEC), told reporters.
"National and international observers will be able to observe the process that will take around three weeks."
He said their staff would work in two shifts auditing around 1,000 ballot boxes a day, with NATO forces helping to transport the boxes from across the country to Kabul.
Shortly after the second round run-off on June 14 Abdullah claimed massive fraud had robbed him of victory and boycotted the vote count by withdrawing his team's observers.
The bitter impasse over the vote to succeed President Hamid Karzai plunged Afghanistan into crisis and raised fears of a return to the ethnic violence of the 1990s.
But on Friday, Kerry flew in and after around 48 hours of intense negotiations with the candidates and Karzai the audit agreement was signed.
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