DIA is led by a Director, typically a three-star military officer. The current director is Lieutenant General Michael D. Maples.

DIA is organized into these primary operational directorates:

Directorate for Human Intelligence (DH): Otherwise knows as Defense HUMINT Service, this directorate manages DIA's and the DoD's human source intelligence collection. This includes the Defense Attache System. Defense HUMINT reportedly controls the Strategic Support Branch, a unit that deploys teams of linguists, field analysts, case officers, interrogation experts, technical specialists, and special forces. It is speculated that Defense Secretary Donald Rumsfeld created the SSB to bypass the limitations of the Central Intelligence Agency after 9/11.

Directorate for MASINT and Technical Collection (DT): Collects measurement and signature intelligence which is any intelligence that does not fit within the definitions of Signals Intelligence, Imagery Intelligence, and Human Intelligence. This often includes radar intelligence, acoustic intelligence, nuclear intelligence, and chemical and biological intelligence. DIA is the central intelligence agency for MASINT collection within the intelligence community.

Directorate for Analysis (DI): Analyzes and disseminates finalized intelligence products for the DIA from all sources as well as from partner Intelligence Community agencies. Analysts focus on the military issues that may arise from political or economic events in foreign countries and also analyze foreign military capabilities, transportation systems, weapons of mass destruction (WMDs), and missile systems and contribute to National Intelligence Estimates and to the President's Daily Brief. The Directorate of Analysis also manages the Armed Forces Medical Intelligence Center and the Missile and Space Intelligence Center. Analysts serve DIA in all of the agency's facilities as well as in the field.

Directorate for Intelligence Joint Staff (J2): Advises and supports the Joint Chiefs of Staff with foreign military intelligence for defense policy and war planning.

Defense Joint Intelligence Operations Center (DJIOC): Fuses tactical, operational, and strategic intelligence assets and serves as the center for coordination of these assets in response to combatant command requirements.

DIA also runs the National Defense Intelligence College.