On the outbreak of war in September 1939, a small photographic interpretation section was attached to the Intelligence Staff of the British Expeditionary Force - GSIa(V), which consisted of three officers trained on an Army Interpretation Course. The key Royal Air Force reconnaissance aircraft - the Bristol Blenheim - was soon found to be inadequate for its long range photographic reconnaissance role and trouble was also experienced with existing camera systems. This meant the only source of long range aerial photography was that provided by the freelance civilian aerial photographer Sidney Cotton using his Lockheed aeroplane.

Cotton persuaded the Air Ministry to give him an assortment of Hudsons, Beechcrafts, Blenheims and even Spitfires for adaptation as photographic reconnaissance aircraft. This small group of aircraft operated from RAF Heston, Middlesex, on secret reconnaissance operations and was officially known as No 2 Camouflage Unit. Cotton, then in the rank of Wing Commander, commanded the unit later known as the Special Flight, and experimented with modified, unarmed Spitfires, flying at heights above 30,000 feet. Cotton sought the aid of his friend Major H Hemming, Managing Director of the Aircraft Operating Company Ltd, an aerial survey firm based at Wembley, Middlesex. The Heston Special Flight, which was renamed the Photographic Development Unit (PDU) in January 1940, continued, unofficially, to use the resources of this company to process and interpret its films and to make detailed drawings with its specialist equipment. After much pressure from the Admiralty, the Air Ministry decided to give the company a formal contract to operate as part of PDU from 1 April and later that month moved its photographic interpretation cell AI1(h) into the company's premises at Wembley. AI1(h) merged with the company in May and on 12 June 1940 the Wembley organisation was given its own identity as the Photographic Development Unit - Interpretation and Intelligence, (PDUI). Major Hemming, now in the honorary rank of Squadron Leader, was placed in charge of the section where he was joined by Squadron Leader Riddell from the Bomber Command photographic interpretation section.

On 18 June 1940 control of PDU and PDUI passed from the Director of Intelligence, Air Ministry, to HQ Coastal Command and on 11 July 1940 a further renaming of the two units took place. PDU was renamed the Photographic Reconnaissance Unit (PRU), and PDUI became the Photographic Interpretation Unit (PIU). During 1940 the accommodation at Wembley was rapidly outgrown and the work was continually disrupted by bombing raids. In April 1941 PIU moved to Danesfield House at Medmenham, Buckinghamshire, and was renamed the Central Interpretation Unit (CIU). Later that year the Bomber Command Damage Assessment Section was absorbed, and amalgamation was completed when the Night Photographic Interpretation Section of No 3 PRU, Oakington, was integrated with CIU in February 1942.

During 1942 and 1943 the CIU gradually expanded and was concerned in the planning stages of practically every operation of the war, and in every aspect of intelligence. American personnel had for some time formed an increasing part of the CIU and on 1 May 1944 this was recognised by changing the title of the unit to the Allied Central Interpretation Unit (ACIU). There were then over 1700 personnel on the unit's strength. In 1945 daily intake of imagery averaged 25,000 negatives and 60,000 prints. By 'VE' day (8 May 1945) the print library, which documented and stored world-wide imagery, held 5,000,000 prints from which 40,000 reports had been produced. The title of the unit reverted to Central interpretation Unit when the Americans returned home in August 1945.