He was knighted in Queen Victoria's Diamond Jubilee year Honours in 1897. The Jewish Chronicle of that time noted "a Ukraine Jew, trained in the schools of European science, saves the lives of helpless Hindoos and Mohammedans and is decorated by the descendant of William the Conqueror and Alfred the Great."
Born Vladimir Aaronovich Chavkin (Russian: Владимир (Маркус-Вольф) Аaронович Хавкин), the fourth of five children of Aaron and Rosalie (daughter of David-Aïsic Landsberg) in a family of a Jewish schoolmaster in Berdyansk, Russian Empire (now Ukraine), he received his education in Odessa, Berdyansk and St. Petersburg.
Young Haffkine was also a member of the Jewish League for Self-Defense. Haffkine was injured while defending a Jewish home during a pogrom. As a result of this action he was arrested but later released due to the intervention of Ilya Mechnikov.
Haffkine continued his studies from 1879 to 1883 with famous biologist Ilya Mechnikov, but after the assassination of Tsar Alexander II, the government increasingly cracked down on people it considered suspicious, including intelligentsia. Haffkine was also employed by the zoological museum at Odessa from 1882 to 1888. In 1888, Haffkine was allowed to emigrate to Switzerland and began his work at the University of Geneva. In 1889 he joined Mechnikov and Louis Pasteur in Paris at the newly established Pasteur Institute where he took up the only available post of librarian.
Haffkine began his scientific career as a protozoologist and protistologist, under the tutelage of Ilya Mechnikov at Imperial Novorossiya University in Odessa and later at the Pasteur Institute in Paris. His early research was on protists such as Astasia, Euglena, and Paramecium, as well as the earliest studies on Holospora, a bacterial parasite of Paramecium. In the early 1890s, Haffkine shifted his attention to studies in practical bacteriology.
The euglenid genus Khawkinea is named in honor of Haffkine's early studies of euglenids, first published in French journals with the author name translated from cyrillic as "Mardochée-Woldemar Khawkine".
At the time, one of the five great cholera pandemics of the 19th century ravaged Asia and Europe. Even though Robert Koch discovered Vibrio cholerae in 1883, the medical science at that time did not consider it a sole cause of the disease. This view was supported by experiments by several biologists, notably Jaume Ferran i Clua in Spain.
Haffkine focused his research on developing cholera vaccine and produced an attenuated form of the bacterium. Risking his own life, on July 18, 1892, Haffkine performed the first human test on himself and reported his findings on July 30 to the Biological Society. Even though his discovery caused an enthusiastic stir in the press, it was not widely accepted by his senior colleagues, including both Mechnikov and Pasteur, nor by European official medical establishment in France, Germany and Russia.
Haffkine considered India, where hundreds of thousands died from ongoing epidemics, as the best place to test his vaccine. Through the influence of Marquis of Dufferin and Ava, who was in Paris as the British Ambassador he was allowed to demonstrate his ideas in England. He proceeded to India in 1893 and established a laboratory at Byculla in 1896 which moved to Parel and was later called the Haffkine institute. Haffkine worked on the plague and by 1902-3 half a million were inoculated but on 30 October 1902, 19 people died from tetanus of 107 inoculated at Mulkowal. This "Mulkowal disaster" led to an enquiry. He was briefly suspended but reappointed director of the Biological Laboratory in Calcutta. He retired in 1915 and suffering from malaria, Haffkine had to return to France.
"Unlike tetanus or diphtheria, which were quickly neutralized by effective vaccines by the 1820s, the immunological aspects of bubonic plague proved to be much more daunting." In October 1896, an epidemic of bubonic plague struck Mumbai and the government asked Haffkine to help. He embarked upon the development of a vaccine in a makeshift laboratory in a corridor of Grant Medical College. In three months of persistent work (one of his assistants experienced a nervous breakdown, two others quit), a form for human trials was ready and on January 10, 1897 Haffkine tested it on himself. "Haffkine's vaccine used a small amount of the bacteria to produce an immune reaction." After these results were announced to the authorities, volunteers at the Byculla jail were inoculated and survived the epidemics, while seven inmates of the control group died. "Like others of these early vaccines, the Haffkine formulation had nasty side effects, and did not provide complete protection, though it was said to have reduced risk by up to 50 percent."
Haffkine's successes in fighting the ongoing epidemics were indisputable, but some officials still insisted on old methods based on sanitarianism: washing homes by fire hose with lime, herding affected and suspected persons into camps and hospitals, and restricting travel.
Even though the official Russia was still unsympathetic to his research, Haffkine's Russian colleagues doctors V.K. Vysokovich and D.K. Zabolotny visited him in Bombay. During the 1898 cholera outbreak in the Russian Empire, the vaccine called "лимфа Хавкина" ("limfa Havkina", Havkin's lymph) saved thousands of lives across the empire.
By the turn of the 20th century, the number of inoculees in India alone reached four million and doctor Haffkine was appointed the Director of the Plague Laboratory in Mumbai (now called Haffkine Institute).
Haffkine was the first to prepare a vaccine for human prophylaxis by killing virulent culture by heat at 60 °C. The major limit of his vaccine was the lack of activity against pulmonary forms of plague.
In 1898, Haffkine approached Aga Khan III with an offer for Sultan Abdul Hamid II to resettle Jews in Palestine, then a province of the Ottoman Empire: the effort "could be progressively undertaken in the Holy Land", "the land would be obtained by purchase from the Sultan's subjects", "the capital was to be provided by wealthier members of the Jewish community", but the plan was rejected.
In 1902, nineteen Indian villagers (inoculated from a single bottle of vaccine) died of tetanus. An inquiry commission indicted Haffkine, and he was relieved of his position and returned to England. The report was unofficially known as the "Little Dreyfus affair", as a reminder of Haffkine's Jewish background and religion.
The Lister Institute reinvestigated the claim and overruled the verdict: it was discovered that an assistant used a dirty bottle cap without sterilizing it.
In July 1907, a letter published in The Times called the case against Haffkine "distinctly disproven". It was signed by Ronald Ross (Nobel laureate, malaria researcher), R.F.C. Leith (the founder of Birmingham University Institute of Pathology), William R. Smith (President of the Council of the Royal Institute of Public Health), and Simon Flexner (Director of Laboratories at New York City Rockefeller Institute), among other medical dignitaries. This led to Haffkine's acquittal.
Published materials from the India Home Department related to the vaccination incident (along with Haffkine's personal diaries on microfilm) are held at the National Library of Medicine in Bethesda, Maryland.
Since Haffkine's post in Mumbai was already occupied, he moved to Calcutta and worked there until his retirement in 1914. Professor Haffkine returned to France and later moved to Lausanne, where he spent the last years of his life. During his brief visit to the Soviet Union in 1927, he found drastic changes in the country of his birth.
Haffkine received numerous honors and awards. In 1925, the Plague Laboratory in Mumbai, Maharashtra was renamed the Haffkine Institute. In commemoration of the centennial of his birth, Haffkine Park was planted in Israel in the 1960s.
In an biography of him, Nobelist Selman Abraham Waksman explains that, in this last phase of his life, Haffkine had become a deeply religious man. Haffkine returned to Orthodox Jewish practice and wrote A Plea for Orthodoxy (1916). In this article, he advocated traditional religious observance and decried the lack of such observance among "enlightened" Jews, and stressed the importance of community life, stating:
A brotherhood built up of racial ties, long tradition, common suffering, faith and hope, is a long tradition, common suffering, faith and hope, is a union ready-made, differing from artificial unions in that the bonds existing between the members contain an added promise of duration and utility. Such a union takes many centuries to form and is a power for good, the neglect or disuse of which is as much an injury to humanity as the removal of an important limb is to the individual... no law of nature operates with more fatality and precision than the law according to which those communities survive in the strife for existence that conform the nearest to the Jewish teachings on the relation of man to his Creator; on the ordering of time for work and rest; on the formation of families and the duties of husband and wife, parents and children ; on the paramount obligations of truthfulness and justice between neighbor and neighbor and to the stranger within the gates.
In addition, in 1929, he established the Haffkine Foundation to foster Jewish education in Eastern Europe. Haffkine was also profoundly respectful of other religions, and "he considered it of the utmost importance to promote the study of the Bible."