Hynek was also a scientific consultant for Project Blue Book, the U.S. Air Force's official study of the UFO mystery from 1948 to 1969. Although Hynek started out as a skeptic and helped the Air Force to debunk most UFO reports, he gradually became convinced that a small number of UFO cases were not hoaxes or explainable as misidentifications of natural phenomena, and that these cases might represent something extraordinary—even alien visitation from other planets. When the Air Force shut down Project Blue Book in 1969, Hynek decided to establish his own organization to continue to study UFO reports in a scientific and unbiased manner.
Started in Evanston, Illinois, but now based in Chicago, CUFOS continues to be a small research organization stressing scientific analysis of UFO cases. Its extensive archives include historically valuable files from defunct civilian research groups such as NICAP, one of the UFO research groups of the 1950s and 1960s. Following Hynek's death in 1986, CUFOS was renamed the J. Allen Hynek Center for UFO Studies in his honor. The current Scientific Director of CUFOS is Mark Rodeghier. Ufologists who have served on the CUFOS Board of Directors are Jerome Clark, UFO historian and author of the "UFO Encyclopedia"; Michael Swords, a retired professor of natural sciences from Western Michigan University; and Thomas E. Bullard, a folklorist at Indiana University.