Musharraf was addressing some 700 delegates at the final session of a joint Afghan-Pakistani tribal assembly in Kabul, following talks with Afghan President Hamid Karzai.
The Pakistani leader called upon the two countries to "develop trust" and to form a united front against Islamic militants.
Karzai responded Musharraf's speech by saying that Pakistan has Afghanistan's trust.
"Pakistan's President made his speech and called for trust. Afghanistan will, with out any doubt, trust its dear brother country and thank Pakistan for its hospitality to Afghan refugees during the past thirty years," Karzai said.
The three-day "Joint Peace Jirga" focused on ways to control cross-border infiltration by militants and how to work together against the Taliban and Al-Qaeda.
A joint declaration was distributed today to participants, calling for measures against terrorism, including rooting out militant training grounds, and for the establishment of a council to push for closer cooperation between the countries.
(with agency reports)
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RFE/RL reporting on Afghanistan, Pakistan, Iraq, Iran, Tatarstan and Bashkortostan, and Central Asia.