"The two leaders will discuss efforts to strengthen the bilateral relationship and build a long-term partnership based on common values," said Mr Bush spokeswoman Dana Perino.
Zardari is the widower of former Prime Minister Benazir Bhutto, who was assassinated last year. He was sworn in as Pakistan's president earlier this month after his predecessor, Pervez Musharraf, resigned following nine years of rule.
The US military sent ground forces into South Waziristan earlier this month without Islamabad's permission. The attack followed an order by President Bush earlier this year authorizing US special forces to carry out ground assaults inside Pakistan without seeking Islamabad's permission.
On Wednesday, Kayani and Pakistan's newly elected prime minister, Yousaf Raza Gilani, met the United States' top military officer, Adm. Michael Mullen, in Islamabad. The US Embassy in Pakistan described the talks as "extremely frank, positive and constructive."
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