He had a conflict with Louis Pasteur

Koch and Pasteur were cordial when they first met at the Seventh International Medical Congress in London in August 1881. But disagreements over science dominated the remainder of their professional lives. Koch's interpretation of the anthrax bacillus he discovered in 1876 as causality that is, the germ that caused the anthrax infections set off the controversy. Although he had not yet developed his postulates, he did not prove that the bacteria was to blame for the illness; rather, he made an inference to that effect. Therefore, Pasteur contended that while Koch's finding did not provide complete proof of causality, his anthrax vaccine created in 1881 did. A remark accompanying Koch's finding that "anthrax never arises without living anthrax bacilli or spores" was published in 1881.

There is in Pasteur's judgment, no more concrete evidence that anthrax bacilli are the actual and exclusive cause of anthrax and that vaccination as Pasteur said is not impossible. Pasteur sent his aide Louis Thuillier to Germany to demonstrate his vaccination and refute Koch's theory. At the International Congress for Hygiene in Geneva in 1882, they engaged in a contentious public dispute during which Koch criticized Pasteur's techniques as "unreliable" and asserted they "are incorrect and they always lead to wrong conclusions." Further criticizing Pasteur, Koch subsequently asserted that "Pasteur is not a physician, and one cannot expect him to make competent judgments regarding pathological processes and the signs of disease."