Mullah Mohammad Omar, in a statement faxed to news organisations in the southern Afghan city of Kandahar, said the Taliban would intensify their war against foreign forces.
"The people of Afghanistan and the Taliban should unite against US and allied forces and intensify their jihad against the foreign occupiers," Omar said in the statement.
The statement was issued on Friday, apparently to mark the end of the Muslim fasting month.
Taliban officials, contacted and questioned about its veracity over the weekend, said it was genuine.
Omar's whereabouts have been a mystery since US-led forces ousted the Taliban in late 2001, after they refused to hand over Osama bin Ladin, architect of the September 11 attacks on New York and Washington.
Omar and Bin Ladin are believed to be hiding out somewhere along the rugged Afghan-Pakistan border.
Omar said in his statement "infidel forces" were trying to capture Muslim countries and make Muslims their slaves. They had committed atrocities against Muslims in Afghanistan, he said.
He also said Afghans had rejected a presidential election last year and parliamentary elections in September.
"The people of Afghanistan rejected the parliamentary and presidential elections but they are showing those elections as a success," Omar said.
"The Taliban are not weak in Afghanistan. We will speed up our jihad"
Mullah Mohammad Omar,
"The Taliban are not weak in Afghanistan. We will speed up our jihad," he said.
The Taliban have stepped up attacks this year but they failed to disrupt the September elections.
More than 1100 people have been killed in violence this year, most of them militants but including more than 50 US soldiers.