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.[9] 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.[9] In the early 1890s, Haffkine shifted his attention to studies in practical bacteriology.[9]