Taussig ended up taking classes at Boston University in histology, bacteriology, and anatomy, without expecting to receive a degree. She had to sit apart from her male colleagues at the back of lecture theatres and was not supposed to speak to them. As an anatomy student at Boston University in 1925, she published her first scientific paper on studies of ox heart muscles with Alexander Begg. With the encouragement of her professor Alexander Begg, Taussig applied to transfer to the Johns Hopkins University School of Medicine, one of the few medical schools to admit women at the time, and was accepted as a full-degree candidate. After completing her MD degree in 1927 at Johns Hopkins, Taussig remained for one year as a cardiology fellow and for two years as a pediatrics intern, and received two Archibald Fellowships, spanning 1927–1930. Taussig wanted to specialise in Internal Medicine, but there was only one position available for a woman in that field, and it was already taken; she therefore decided to specialise in pediatrics, and ended up working in pediatric cardiology, a field that was still in its infancy.