In Hahnemann's time, the only vaccination known was for smallpox. Infecting people with pus from a smallpox vesicle was an ancient practice used in parts of the Middle and Far East. It was known in Britain through diplomatic contacts at the Sultan's palace in Constantinople. Its modern use in the West dates from the discovery by Edward Jenner, an English country doctor, that milkmaids who had had cowpox seemed to get a milder form of smallpox. This led him to infect people with pus from a cowpox vesicle, and within a century the practice had spread widely in Europe in an attempt to combat the recurrent epidemics. The term "vaccination" dates from this connection with cows; the Latin word vacca means cows.

The debate over the efficacy of vaccination began there, with some arguing the practice only spread smallpox and others arguing that it was the only means of prevention against this dread disease. Jenner's efforts to prevent disease by means of a weakened form of the same or a similar disease would later inspire others, most notably Pasteur, the father of modern vaccination theory and therapy. Pasteur represents the branch of Western medicine interested in prevention, but on the basis of the germ theory of disease. The body is largely seen as subject to invasion from external germs which the body's immune system must then fight off. In the process, the body somehow gains life-long immunity to further infection.

The idea behind vaccination is to provide the body with this coveted immunity without the risk of contracting the natural disease agent. This is accomplished by artificially introducing a weakened form of that agent into the body. Immunity is equated with white blood cells which remain ready to attack once the wild virus is encountered. However, there is research emerging which questions this reliance on white blood cells as a true indicator of immunity. Studies have shown that children with high titre counts after vaccination still contracted the disease whereas those unvaccinated with low or non-existent counts did not. These studies suggest that other aspects of the immune system, including the skin and respiratory system are involved.

Hahnemann's Views

Hahnemann wrote little about vaccination, but he recognized in the Organon, starting with the first edition in 1810, that the practice of vaccination against smallpox was an example of the law of similars. Most of his references relate to the validity in nature of the law of similars, namely that two similar diseases cannot naturally co-exist in the same person. In Aphorism 46 he states: ". . . the cow-pox when near maturity does, on account of its great similarity, homeopathically diminish very much the supervening smallpox and make it much milder . . ."

Later, in the Sixth Edition, he added the following footnote:

This seems to be the reason for this beneficial remarkable fact, namely that since the general distribution of Jenner's Cow-Pox vaccination, human smallpox never again appeared as epidemically or virulently as 40-50 years before when one city visited lost at least one half and often three-quarters of its children by death of this miserable pestilence.

In the same Aphorism, Hahnemann speaks of the fact that cowpox produces a type of eruption and then goes on to say:

 . . . the inoculated cow-pox, I say, after it has taken, cures perfectly and permanently, in a homeopathic manner, by the similarity of this accessory miasm [the cow-pox], analogous cutaneous eruptions of children, often of very long-standing and of a very troublesome character . . .

Hahnemann seems to have considered that the Jennerian method of vaccination – scratching cowpox pus into the skin – was both preventative in epidemics and curative when it was used against similar disease states.

Hahnemann does not go on to say whether he felt that there were any detriments to this approach which involved actual disease matter. However, this can be extrapolated from his general views on the prescribing of medicines, e.g. to avoid drug-induced illness, medicines must be given in the smallest dose possible (meaning highly diluted and succussed), and according to the individual susceptibility of the patient. These conditions were not met by the vaccination of Hahnemann's day, nor of more recent times.

It is possible that Jenner's vaccination suggested to homeopaths, Hahnemann among them, the use of disease matter in potentised form. At the end of his life Hahnemann accepted Hering's first nosode, now known as Psorinum. Hahnemann's Chronic Diseases gives his view of the homeopathicity of nosodes:

I say homeopathic use, for it does not remain idem (the same); even if the prepared itch substance should be given to the same patient from whom it was taken, it would not remain idem (the same), as it could only be useful to him in a potentised state . . . But the dynamization or potentizing changes it and modifies it . . . Thus potentised and modified also, the itch substance (Psorin) when taken is no more an idem (same) with the crude original itch substance, but only a simillimum (thing most similar). For between IDEM and SIMILLIMUM there is no intermediate forany one that can think  . . .

Hahnemann must have worried about the ramifications of an approach involving nosodes and later reversed his position. He subsequently stated that the use of nosodes made from the same disease matter was not homeopathy, but isopathy (the principle of like, rather than similars). However, this did not deter Hering and others from continuing to experiment with nosodes.

J. Compton Burnett and Vaccinosis

The next critical reference to vaccination came in the form of a small booklet entitled Vaccinosis by J. Compton Burnett, an iconoclastic British homeopath of the late 19th century. Here he raised, for the first time in the English homeopathic literature, the idea that vaccination can inculcate a disease state onto the vital force, which Burnett called "vaccinosis." He distinguished this from the well-known immediate reactions to vaccination, then known as "vaccinia." Burnett's views were based on articles in the German homeopathic journals which he read widely and fully credited (admirably following Hahnemann in his willingness to acknowledge intellectual debts).

Burnett's ideas formed the basis of the homeopathic view of vaccination. In Burnett's time, as in Hahnemann's, vaccination meant the use of cowpox or attenuated smallpox. Burnett promoted the discoveries of German homeopaths such as Rummel, Boenninghausen, Grauvogel, Kunkel, and Goullon, who spoke of the ill-effects of smallpox vaccination and the use of Thuja to cure it. He credits Boenninghausen as the first to notice the homeopathicity of Thuja to smallpox, and Kukel and Goullon with using this observation to treat the ill-effects of vaccination.

Burnett was the first to forcefully state the dangers of vaccination, or the use of actual disease matter to try to protect against serious disease states. This zeal led to Burnett's castigation of Koch for his disasterous application of material doses of the tuberculosis germ. Koch was forced into exile in Egypt, where he proposed the use of a homeopathic potency of the germ, which he called Tuberculinum.

For Burnett, vaccination generated a state of disease. This is due to the fact that it is pathogenic material. That it is given to protect does not detract from the fact that it is also disease-generating. If a vaccination works, then it does because it generates a response on the part of the vital force, on account of its homeopathicity to a latent weakness in the vital force. This weakness is the sycotic miasm of Hahnemann, whose main remedy against it and gonorrhea was also Thuja.

Burnett introduced the radical idea that the vaccine reaction, vaccinia, was not the sign of whether a vaccination had "taken," i.e., had been successful. Burnett argued that if the vital force mounted a strong response to the vaccination, through local reactions and fever, then the vital force was strong enough to fight it and the full natural disease. He also argued that if the person did not respond to the vaccination – the prophylaxis did not "take" – it was because the vaccination had implanted itself on the vital force as a disease state, representing a serious condition leading to chronic problems he termed vaccinosis.

The vaccinated person is poisoned by the vaccine virus; what is called the 'taking' is, in point of fact, the constitutional re-action whereby the organism frees itself more or less from the inserted virus. If the person do [sic] not 'take', and the VIRUS HAS BEEN ABSORBED, the 'taking' becomes a chronic process – paresis, neuralgias, cephalalgias, pimples, acne, &c. The less a person 'takes', therefore (in such a case), the MORE is he likely to suffer from chronic vaccinosis, i.e., from the genuine vaccination disease in its chronic form, very frequently a neuralgia or paresis. (J. Compton Burnett, Vaccinosis, p. 22)

For Burnett, any protection afforded by vaccination could only be by the creation of a disease state rendering the vital force no longer susceptible, as it normally would be, to responding to the natural disease agent. And this "protection" comes at the cost of a deep grip on the internal economy:

The vaccinate is one who is suffering from vaccinosis . . . it is his diseased condition that protects him from small-pox.  . . . Hence I must call attention to what I believe is fact, viz.: that it often does take deep hold of the constitution without calling forth any local phenomenon. (Burnett, ibid, p. 20)

Burnett also made several other important points regarding vaccination:

1. Vaccination protection results in a decrease in the number of people catching the disease state (morbidity rate), but does not really change the rate at which people die from it (mortality rate). He argued this was due to the fact that the vaccination, which was a weaker form of the disease, only protected people who had a low susceptibility to the disease state and did not really protect those who were very susceptible.

2. Vaccination protection varies over time and according to dose. This means that epidemics will still occur with regularity.

3. Vaccination is not homeopathy because homeopathy is a system of cure, not prevention, but that vaccination does operate on the principle of similars and, thus, can be more properly called "homeoprophylaxis."

4. Vaccination as practiced by Pasteur and Jenner, using material doses, will eventually end in disaster because it is temporary protection, does not individualize the dose, and brings long-term chronic consequences. Also, it will actually increase the mortality rate because in addition to the vaccinosis, if the person also catches the disease the prophylaxis was intended to prevent, he is more likely to die than if he had just caught the disease without the vaccination.

5. The only safe way to effect homeoprophylaxis is through potentisation of the disease agent. Burnett saw this as essential. He does not say, but seems to imply, that even homeopathic prophylaxis is temporary and reduced in time by the vital force re-asserting health.