Photo-interpreters scanned the many U-2 pictures and discovered that the SAM sites were part of a familiar pattern. They had seen pictures of the layout before, taken over Russia. It was a launching site for mobile medium-range ballistic missiles, and the SAM sites were located to defend them. Further, the anti-aircraft missiles were on launchers, ready for firing.

It was a new ball game. There was a potential risk of losing a U-2 and another Powers incident. Defence Secretary Robert S. McNamara made the decision to have further U-2 flights made by USAF pilots from Strategic Air Command. It was a fine distinction; the U-2 pilots employed by the CIA were all recent transfers from the military services, and ostensibly civilians.

After a quick checkout in the U-2, Majors Rudolf Anderson, Jr, and Richard S. Heyser, of SAC's 4080th Strategic Reconnaissance Wing at Laughlin AFB, Texas, climbed into the polished gray airplanes on 14 October. They flew southeast, made their landfalls, and then crossed the island on coordinated flight paths that covered the suspect area around San Cristobal in detail and duplicate. Both were within range of the Cuban SAMs at times, but neither was fired upon.

The U-2s carried back pictures of a medium-range ballistic missile field site. Seven missiles were on parked transporters outside of shelters, and an eighth was parked next to one of the four erectors on the site. Propellant loading equipment was standing by. At a second site, the cameras caught six missile transporters that had been parked in the shade, and a Russian truck convoy moving into the site.

Now the reconnaissance task became two-fold. It had to photograph all of Cuba from high altitude, pinpointing existing sites and at the same time searching for others under construction. When specific objectives had been located by this technique, low-flying reconnaissance aircraft would be dispatched to get detailed pictures.