The function of the immune system is to recognize foreign elements and identify them as normal or potentially harmful. The first step in this discrimination is surveillance by antigen-presenting cells (APCs), which are present throughout the body. Factors that affect the immunogenicity of a molecule include the presence of an adjuvant, the depot effect, the frequency of the antigen administration, and the quantity of the material administered.

For the various types of botulinum toxin, the issue of the effect on efficacy is particularly relevant to antibody formation. An antibody to one type of botulinum toxin may potentially bind to an antibody of a different type. Safety issues with therapeutic proteins involve allergic responses, as well as formation of immune complexes and the subsequent immune complex disease. The concerns with botulinum toxins primarily relate to the potential for inhibiting efficacy.

Protein therapeutics are important only if the antibodies have been generated against the administered therapeutic. This differs for the types of botulinum toxin. In the development of botulinum toxin type B, the factors that might increase the likelihood or magnitude of an immune response were considered and eliminated as much as possible. Only antibodies to the neurotoxin protein impact efficacy or safety.