The NIH continued to deny Dr. Stewart’s funding to study cancer, so she took a temporary position at a hospital in Staten Island to gain more experience. Finally, after an appointment to medical director in the United States Public Health Service (PHS) Commissioned Corps and a position at the National Cancer Institute (NCI) in Baltimore, the NIH accepted her request to study cancer. She returned to the NIH in 1951 to work at their National Cancer Institute ( NCI). Dr. Stewart was the Head of the Human Virus Studies Section in the Laboratory of Viral Oncology at the NCI at the NIH.

In 1956 she isolated the SE (Stewart-Eddy) polyoma virus with Dr. Bernice Eddy of the Division of Biologics Standards (DBS) Laboratory of Virology & Rickettsiology. The SE polyoma virus induces parotid gland tumors and a variety of other primary neoplasms in mice and other animals, which had implications for future viral oncology research.