The ISI has for decades maintained contacts with various militant groups in the tribal areas and elsewhere, both for gathering intelligence and as proxies to exert influence on neighboring India and Afghanistan. It is unclear whether the C.I.A. officials have concluded that contacts between the ISI and militant groups are blessed at the highest levels of Pakistan’s spy service and military, or are carried out by rogue elements of Pakistan’s security apparatus.
http://www.nytimes.com/2008/07/30/world/asia/30pstan.html?_r=1&partner=rssnyt&emc=rss&oref=slogin
