Kafatos was sponsored by Anne Gruner Schlumberger to study in the United States of America. He received a Bachelor of Science degree from Cornell University, and a Doctor of Philosophy from Harvard University on entomology in 1965.
He remains Honorary President of the European Research Council. At the beginning of his career, he contributed to the development of the Complementary deoxyribonucleic acid (cDNA) cloning technology and worked on the mechanisms of cellular differentiation leading to the formation of the eggs in insects. He has particular interest in malaria research and used his knowledge of the genetics and molecular biology of insects to understand how the insect vector copes with the Plasmodium parasite. He was Assistant Professor and later Professor and Chairman of the department of Cellular and Developmental Biology of Harvard University, Professor of Biology at the University of Athens and at the University of Crete, director of the Institute of Molecular Biology and Biotechnology (IMBB) of the Foundation for & Technology – Hellas in Heraklion and third Director-General of the European Molecular Biology Laboratory from 1993 to 2005.
Since 2005, he has been a professor at Imperial College in London.
Since 2008, he is the President of the European Council. Fotis Kafatos is an influential Greek biologist, having had a pivotal role in triggering the interest of the Greek government for Science, with the establishment of the Faculty of Biology in the University of Athens, the Faculty of Biology in the University of Crete and the IMBB in Heraklion.
Royal Society; Pontifical Academy of Sciences. National Academy of Sciences. French Academy of Sciences]
Between 2005-2010 he was the founding president of the European Council (European Research Council) and member of its Scientific Council.
He is a member of the Royal Society of London, the Pontifical Academy of Sciences, the Académie des Sciences, the National Academy of Sciences (since 1982), the European Molecular Biology Organization (European Molecular Biology Organization).