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In August 1954, Dr. Bernice Eddy had been testing a batch of polio vaccines from Cutter Laboratories and when she noticed that the vaccine had given polio to a test monkey. She found that three of the six samples had paralyzed test monkeys. Dr. She Eddy knew something was wrong and brought it to the attention of her supervisor, Dr. William Workman. Because of the previous polio epidemics and the race to create a vaccine, Dr. Eddy and her team had been working around the clock testing the Salk vaccine. Amidst the scientific and bureaucratic chaos, Workman never told the licensing committee, and the Cutter vaccine was approved and shipped out. In the spring of 1955, the year following a field trial that showed the Salk inactivated (killed) polio vaccine to be safe and effective, DBS licensed several firms to produce the vaccine. One, Cutter Laboratories , accidentally released vaccine that retained live polio virus, resulting in 260 paralytic cases of the disease, a disaster that caused panic among parents and scientists alike. Amidst the controversy, Dr. Eddy was relieved of her polio control testing duties in 1955 but continued to work in biologics. Dr. William Workman was also forced out of his job as head of the Laboratory of Biologics Control (predecessor to DBS, which Dr. Roderick Murray would head beginning in 1955) but stayed on as Chief of the Laboratory of Control Activities until he retired in 1963. The NIH Director at the time, William H. Sebrell Jr., also resigned in 1955, amidst the Cutter controversy.

In 1956 she worked with Dr. Sarah Stewart of the National Cancer Institute, and they identified the S-E (Stewart-Eddy) polyoma virus, which can cause tumors. Dr. Eddy also identified the simian virus 40 (SV-40). Her work led to the newborn hamster being the preferred animal for testing potentially oncogenic viruses of mammalian origin. Twice Drs. Stewart and Eddy were nominated for the Nobel Prize for their work on the S-E polyoma virus, but unfortunately, they never won.

In February 1961, Dr. Murray informed Dr. Bernice Eddy that her research interests conflicted with her control work on respiratory viruses and that going forward she would be asked to spend time solely on research, and that her staff would be reduced. She refuted this claim and wrote back to the Chief of the Control Activities, Dr. William Workman. She then received a memo in reply from Dr. Joseph Smadel, the Chief of the Laboratory of Virology and Rickettsiology, who told her she was being forced to vacate her current position. It seemed that as long as Dr. Eddy was engaged in basic research with only minor relevance to her control activities, she was allowed to continue her work. But , but if her research began to identify factors which might require changes in regulatory control of vaccines, her work was to stop. In July 1961, Dr. Eddy began her new role in research only. Much of the treatment of Dr. Eddy was revealed in the hearings in Congress as part of the Consumer Safety Act of 1972.

Beginning in July 1961, Dr. Eddy was the Chief of the Section on Experimental Virology within the Laboratory of Virology & Rickettsiology in the DBS.  This This was her new research-only role that kept her out of control activities for vaccines.

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