Gabriel Bertrand, with Roux's authorization, crafted a grenade based on chloropicrin and Fourneau discovered the chemical reaction that led to the formation of methylarsine chloride.

"[6] In 1938 the institute, despite its relative poverty, built a biochemical division and another one dedicated to cellular pathology, whose direction was entrusted to the hands of Boivin (who went on to discover endotoxins that are contained in the germ's body and are freed after its death).

[2]: 205  The general mobilization after France's declaration of war against Germany, in September 1939, emptied the Institute and significantly reduced its activities, as members of appropriate age and condition were recruited into the army, but the almost total absence of battles during the first months of the conflict helped maintain the sanitary situation on the front.

After the occupation of France, the Germans never tried to gather information from the institute's research; their confidence in Germany's advantage in this field decreased their curiosity, and their only interest was in the serums and vaccines that it could provide to their troops or the European auxiliaries they recruited.

[2]: 209–210  The cause of the epidemic was later found to be due to a member of the Institute stealing a culture of the germ responsible for the disease and, with the collaboration of an accomplice, infecting a large quantity of butter used to feed German troops.

The institute was not a location for German entrenchment even during the battles for Paris's liberation because of the honor and respect it commanded, as well as out of fear that involving it in any type of conflict might "free the ghosts of long defeated diseases".

Roux and Yersin established that they were dealing with a new type of bacillus, not only able to proliferate and abundantly reproduce itself, but also capable of spreading at the same time a powerful venom, and they deduced that it can play the role of antigen, that is if they could overcome the delicate moment of its injection, made especially dangerous by the toxin.

Nonetheless, Roux was not convinced by this result, since no one knew the collateral effects of the procedure, and preferred to use serotherapy since more than one lab study – like the one accomplished by Charles Richet – demonstrated that the serum of an animal vaccinated against the disease included the antibodies needed to defeat it.

Once the results were made public by Le Figaro newspaper, a subscription fund was opened to raise the money needed to provide the Institute with the number of horses necessary to produce enough serum to satisfy the national demand.

[2]: 128  The sexually transmittable Treponema pallidum (the syphilis germ), detected by two German biologists, Schaudinn and Hoffmann, affects only the human race – where it resides in sperm, ulceration, and cancers that it is able to cause – and, as it would later be discovered, some anthropoid apes, especially chimpanzees.

Both Roux and Metchnikoff, following the discovery that this type of ape can be contaminated with the illness, contributed with their research in creating a vaccine, while Bordet and Wassermann elaborated a solution that was able to expose the germ's presence in human blood.

German biologists opposed to his doctrine the humoral theory: they claimed to have found in Roux's serum some substances able to reveal the presence of microbes, and to ensure their destruction if properly stimulated.

The news of a violent plague outburst in Yunman enabled Yersin to show his potential as he was summoned, as Pasteur's scholar, to conduct microbiological research of the disease.

Yersin looked for the germ responsible for the infection specifically in these plague spots, tumors caused by the inflammation of the lymphatic glands which become black because of the necrosis of the tissue.

Right after he had discovered the bacillus, Koch had tried in vain to create a vaccine against it, however, the injection of the filtrate he had prepared, later called tuberculin, had the effect of revealing who was phthisic from who was not by causing in the latter—and not in the former—fever and light trembling.

Having observed that most actinomycetales are saprophytes, that are able to survive outside of living organisms, with the help of a veterinarian, Camille Guerin, he attempted to create an environment for the bacillus that, in time, altered its features by eliminating the virulence and leaving only the antigenic power.

The environment deemed appropriate for the denaturation of the Mycobacterium bovis was a compost of potatoes cooked in the bile of an ox treated with glycerine, and Calmette re-inseminated it every three weeks for thirteen years while checking for an enfeeblement of the pathogenic power of the bacillus.

[2]: 186 In Saigon Albert Calmette also created the first overseas branch of the institute, where he produced an amount of smallpox and rabies vaccines sufficient to satisfy the needs of the population and started a study on venomous snakes, particularly cobras.

[2]: 98 The scientist and writer Charles Nicolle while in Tunis studied how epidemic typhus – known for the red spots it left on sick people that disappeared before their death – was transmitted.

The cause of the disease, a bacillus that was discovered almost twenty years before by the German bacteriologist Karl Joseph Eberth and that looks like a bodiless spider, was constantly present in this river and not even pouring extensive quantities of ozone and of lime permanganate into its water was enough to exterminate the bacteria.

After working in the rabies division of Rue Vaquelin and studying the microbe that causes dysentery, André Chantemesse collaborated with a younger bacteriologist, Georges-Fernand Widal.

[18][19] The Hospital Pasteur was built during the first years of the 20th century in front of the institute and was employed for a long time by the members as a field for clinical observation and experimentations of therapeutical processes elaborated by themselves.

The construction of the hospital was enabled by the gift of a benefactor, Madame Lebaudy, while money offered by the baroness Hirsch was used to build a large pavilion that accommodated the Department of Chemical Biology of the institute.

It was critical in resolving a controversy aroused between Pasteur and Berthelot after the publication of Claude Bernard's posthumous essay regarding the nature of the agents implicated in some transformations that happen inside plants, like fermentation.

Duclaux's study on the metabolism of nutrients did not have immediate practical applications, but later revealed how extensive is the field of enzymes and opened new roads that would lead biology to extend the knowledge on life's mechanisms on a molecular level.

Other research in progress includes the study of cancer and specifically the investigation of the role of oncogenes, the identification of tumor markers for diagnostic tests, and the development of new treatments.

Currently, an extensive line of research aims at determining the complete genome sequences of several organisms of medical importance, in the hope of finding new therapeutic approaches.

The book The Paris Option by Robert Ludlum and Gayle Lynds begins with four men blowing up the Institut Pasteur, as a cover for stealing a molecular computer project being done there.