At first, other scientists in the field of X-ray crystallography ignored or criticized this new method. The method involved time-consuming calculations and mathematical expertise, unfamiliar to most crystallographers. But in the 1960's, as computers and special programs to deal with the Hauptman-Karle method were introduced, the direct method gained widespread acceptance. It has allowed scientists to determine the atomic structures of far more substances, in far less time, than would have been possible using other methods.
Hauptman continued to work with Karle at the Naval Research Laboratory until 1970. Hauptman then became professor of biophysics at the State University of New York at Buffalo. His book Crystal Structure Determination: The Role of the Cosine Seminvariants was published in 1972. In the 1990's, Hauptman assumed an additional position at the university as professor of computer science.
Hauptman joined a crystallographic research group at the Medical Foundation of Buffalo (MFB) in 1970. He became its vice president and director in 1972 and its president in 1988. At the MFB, he continued his work on the direct method. In the 1990's, Hauptman and his colleagues introduced a new computer program that could determine chemical structures in substances of up to several hundred atoms within a few hours or days. In 1994, the MFB changed its name to the Hauptman-Woodward Medical Research Institute. In addition to his position as president, Hauptman has served on the institute's board of directors since 1999.
Hauptman received the Pure Science Award from the Scientific Research Society of America in 1959 and the Schoellkopf Award from the American Chemical Society in 1986. He lives in Buffalo, New York.