Waller left Bonn in 1856, and went to Paris to continue his work in Flourens's laboratory at the Jardin des Plantes; but he soon contracted some form of infection, which left him an invalid for the next two years. He returned to England, and, his health improving, he accepted in 1858 the appointment of professor of physiology in Queen's College, Birmingham (a predecessor college of Birmingham University), and the post of physician to the hospital. These appointments he did not long retain. The heart affection which eventually proved fatal led him to seek rest, and, after staying two years longer in England, he retired first to Bruges and afterwards to Switzerland.