In 1900, he left Paris to found the Pasteur Institute in Brussels, and made his discovery that the bacteriolytic effect of acquired specific antibody is significantly enhanced in vivo by the presence of innate serum components which he termed alexine (but which are now known as complement).
With Octave Gengou, he isolated Bordetella pertussis in pure culture in 1906 and posited it as the cause of whooping cough.