Taussig later became an associate professor at the Johns Hopkins School of Medicine; she was promoted to full professor in 1959. At the time, she was only the second woman to reach full professor status at the university. She continued to serve as the director of the Harriet Lane Home (the children's treatment and research centre at Johns Hopkins) until her retirement in 1963. Most paediatric clinics at the time focussed on rheumatic fever, which was the major source of child mortality, but because of Taussig's experience, the Harriet Lane Home was also able to provide specialist care for children with congenital heart disease. It became a world-leading centre that aspiring surgeons flocked to.