President Bush praised President Musharraf as a key ally in the 'war on terror' on the last leg of his South Asia tour.
Despite the praise Mr Bush deftly batted away Pakistan's requests for a nuclear deal and the Kashmir issue.
The first ladies also met and Mrs Musharraf raised the issue of admission of more Pakistani women to US universities.
Mr Bush's visit was not welcomed by many people who demonstrated across the country.
There were protests against the US involvement in Iraq and the cartoons of the Prophet Mohammad.
Members of the party of former Pakistani cricketer Imran Khan were arrested ahead of Mr Bush's visit.
Security was tight during Mr Bush's visit especially following a bomb blast at the US consulate in Karachi on Thursday.