ISI is headquartered in Islamabad and works under a Director General, a serving Lieutenant General of the Pakistan Army.

There are three Deputy Director Generals-designated DDG (Political), DDG (External) and DDG (General).

The ISI is staffed mainly by personnel deputed from the police, para-military forces and some specialized units of the Army.

There are over 25,000 active men on its staff. This figure does not include informants and assets. It is organized into six to eight divisions .

Joint Intelligence X: JIX
It serves as the secretariat which co-ordinates and provides administrative support to the other ISI wings and field organizations. It also prepares intelligence estimates and threat assessments.It provides administrative support to the other major divisions and regional organizations of the ISI.

Joint Intelligence Bureau (JIB)
One of the largest and most powerful divisions of the ISI, monitors political intelligence.The JIB consists of three subsections, with one subsection devoted to operations involving India, other operations involve, anti-terrorism and VIP security.

Joint Counter Intelligence Bureau (JCIB
Responsible for oversees intelligence operations in Central Asia South Asia, Afghanistan, the Middle East, Israel and Russia also responsible for field surveillance of Pakistani diplomats stationed abroad, if need be monitoring foreign diplomats as well .

Joint Intelligence/North (JIN)
Conduct ISI operations for Jammu and Kashmir , including monitoring Indian forces deployed within disputed Kashmir forcefully held by India.

Joint Intelligence Miscellaneous (JIM)
Responsible for covert offensive intelligence operations and war time espionage.

Joint Signal Intelligence Bureau (JSIB)
It includes Deputy Directors for Wireless, Monitoring and Photos, operates a chain of signals intelligence collection stations, and provide communication support to its operatives. It aslo collects Intelligence through monitoring of communications channels of neighboring countries.It has a chain of stations that track and collect intelligence signals along the Indo-Pakistani border, and it provides communications assistance for freedom campaigns in Kashmir.

A sizeable number of the staff is from the Army Signal Corps. It is believed that it has its units deployed in Karachi, Lahore and Peshawar.

Joint Intelligence Technical (JIT)
It is believed that JIT include a separate explosives section and a chemical warfare section.

The ISI maintains one more primary sections in addition to the seven outlined above that is the Joint Intelligence Technical division.

At first, the ISI focused primarily on domestic espionage, such as tapping telephone conversations and monitoring internal political affairs.

Because of its narrow scope, it was reportedly unable to locate an Indian armored division during the Indo-Pakistani War in 1965. When the war was over, Ayub appointed General Yahya Khan to chair a committee to evaluate the ISI and its subdivisions.

From 1983 to 1997, the ISI reportedly trained over 80,000 Afghan Mujahideen for campaigns in Afghanistan. During the 1990s, the ISI grew into a powerful organization.

It is said to function as an invisible government and is frequently called “a state within a state.

On September 2001, President Musharraf appointed a new Director General for ISI, Lieutenant General Ehsanul Haq