Mary Waye received a bachelor of science with honours from University of Western Ontario, majoring in bacteriology and immunology. She then took graduate work and received a PhD in medical biophysics at University of Toronto. She received support as a research student of the National Cancer Institute. In completing her PhD, she received a King George V Fellowship and received her post-doctoral training at the Medical Research Council in Cambridge as a National Cancer Institute Research Fellow. She did research in the Division of Protein and Nucleic Acid and later also received training in the Division of Structural Studies in Cambridge. She returned to University of Toronto as an assistant professor. She has been at Chinese University of Hong Kong since 1992. She was appointed as the Founding Director of the Croucher Laboratory for Human Genomics in 2004.