In 1842 Stokes became Regius Professor of Physic in Dublin University, in succession to his father. From this time, though he contributed occasional papers, lectures, and cases of value to the _Dublin Journal of Medical Science_, and to the medical societies, he published no book till 1854, when a valuable treatise on Diseases of the Heart confirmed his reputation. In this he paid great attention to functional disturbances of the heart, where no organic disease was present. He says with great modesty, “the diagnosis of the combinations of diseases, even in so small an organ as the heart, is still to be worked out.... As the student fresh from the schools, and proud of his supposed superiority in the refinements of diagnosis, advances into the stern realities of practice, he will be taught greater modesty, and a more wholesome caution. He will find, especially in chronic disease, that important changes may exist without corresponding physical signs—that as disease advances its original special evidences may disappear—that the signs of a recent and trivial affection at one portion of the heart may altogether obscure, or prevent, those of a disease longer in standing and much more important—that functional alteration may not only cause the signs of organic lesion to vary infinitely, but even to wholly disappear—that the signs on which he has formed his opinion to-day may be wanting to-morrow; and, lastly, that to settle the simple question between the existence of functional and that of organic disease, will occasionally baffle the powers of even the most enlightened and experienced physicians.” This treatise is acknowledged to be one of the most acute, graphic, and complete accounts of the clinical aspects of heart disease. In 1854 also he published a series of lectures on Fever in the _Medical Times and Gazette_, which were collected into a volume, with additions in 1874. Here he showed himself as still sceptical of the advances made by Jenner, Murchison, and others. As he wrote in one of the lectures, “there is nothing more difficult than for a man who has been educated in a particular doctrine to free himself from it, even though he has found it to be wrong,” and he could never free himself from Alison’s strong belief that fevers were essentially alike.