The purpose of this study was to identify the location of domains within the serotype A neurotoxin of Clostridium botulinum (BoNT/A) that conferred protection against botulism. The BoNT/A gene was subcloned into a series of 10 overlapping fragments that were expressed in Escherichia coli. The expressed proteins were partially purified and used to immunize mice. The resulting antisera were screened by immunoblotting analysis for the presence of BoNT/A-specific antibody. All fragments, except one, elicited antibody that recognized BoNT/A in an immunoblot. Serological screening identified several fragment-specific cross-reactive epitopes that were shared by heterologous serotypes of BoNT. Most of these epitopes immunoreactive by enzyme-linked immunosorbent assay, but not by immunoblot. Only two fragments were shown to confer protection against BoNT/A intoxication. Both of these proteins were derived from segments of the heavy chain and encoded amino acid residues H455-661 and H1150-1289 of BoNT/A.