Donahoe has published over 230 peer-reviewed publications in developmental biology, concentrating on Mullerian Inhibiting Substance as a potential anticancer agent against human ovarian carcinomas, as well as the genetics of sex differentiation and a number of other congenital anomalies for which she has been steadily funded by the NIH. She and her colleagues, particularly David MacLaughlin, hold a number of patents on MIS. They purified the human MIS, cloned the MIS gene and that of its receptors, studied their regulation and their roles in the growth, diagnosis, and treatment of ovarian and other reproductive tumors, and used MIS as a marker in the diagnosis of human tumors in human intersex disorders.

Donahoe is a member of the National Academy of Sciences, Institute of Medicine of the National Academy of Sciences, and American Academy of Arts and Sciences. She served as President of the Boston Surgical Society and is President-elect of the American Pediatric Surgical Association. She has received many research prizes and honorary degrees for her work on MIS but her fondest dream is to see it developed as a therapeutic for ovarian and other reproductive cancers.