Theory of disease
The conventional theory of disease in Hahnemann's time was based on the four humours. Mainstream medicine focused on restoring the balance in the humours, either by attempting to remove an excess of a humour (by such methods as bloodletting and purging, the use of laxatives, enemas and nauseous substances that made patients vomit) or by suppressing symptoms associated with the humours causing trouble, such as giving feverish (and so hot and wet) patients substances associated with cold and dry.
The late 18th century was a time of intense exploration, with many new diseases being identified, and the model of internal humours was proving inadequate. For example, many new diseases were clearly associated with certain geographic regions, which was difficult to explain through entirely internal mechanisms. Scientists were considering a model of external causes, and Hahnemann was lead to speculate on such causes of disease.
Beginning with his early work, Hahnemann rejected the prevailing physical model, in favour of a view of disease as more dynamic or spirit-like. He came to consider the spiritual factors as the root cause of all disease, in what he termed the "highest disease." Most later homeopaths, in particular James Tyler Kent, have tended to put even more emphasis on spiritual factors.
Vitalism had been a part of mainstream science through the 18th century. Whereas modern medicine sees bacteria and viruses as the causes of many diseases, some modern homeopaths regard them as effects, not causes, of disease. Others have to some extent adapted to the views of modern medicine by referring to disturbances in, and stimulation of, the immune system, rather than the vital force.
Scientific medicine has discarded vitalism and its associated beliefs in favour of the germ theory of disease, as part of a physiological model based on the work of scientists like Louis Pasteur, Alexander Fleming, and Joseph Lister. Moreover, following Avogadro's discovery it has firmly rejected the possibility of most homeopathic preparations having any medicinal action.