Duclaux recommended Roux to Louis Pasteur, who was looking for assistants, and Roux joined Pasteur's laboratory as a research assistant from 1878 to 1883 at the École Normale Supérieure in Paris. When Roux first began his career with Pasteur, he started as an animal inoculator. He performed well in the technical tasks, and became more involved with research. Roux began his research on the microbiological causation of diseases, and in this capacity worked with Pasteur on avian cholera (1879–1880) and anthrax (1879–1890), and was involved in the famous experiment on anthrax vaccination of animals at . In this vaccination experiment, Pasteur and Roux injected 25 sheep with their anthrax vaccine, and the other 25 were unvaccinated. All 50 sheep were injected with the anthrax bacillus. All 25 vaccinated sheep survived, and all 25 unvaccinated sheep died, just as Pasteur and Roux predicted.