The purpose of this work was to map, on the heavy (H) chain of botulinum neurotoxin A (BoNT/A), the regions that bind to mouse brain synaptosomes (snps). We prepared 60 synthetic overlapping peptides that had uniform size and overlaps and encompassed the entire H chain (residues 499 to 1296) of BoNT/A. The ability of each peptide to inhibit the binding of 125I-labeled BoNT/A to mouse brain snps was studied. The binding of 125I-labeled BoNT/A to mouse brain snps was completely inhibited by free unlabeled BoNT/A, but not by unrelated proteins, indicating that the binding of BoNT/A to mouse brain snps was a specific event. Inhibition studies with the individual peptides showed that, on the H(N) domain, inhibitory activities greater than 10% were exhibited, in decreasing order, by peptides 799-817, 659-677, 729-747, 533-551, 701-719, and 757-775. Lower inhibitory activities (between 5.6% and 8.7%) were exhibited by five other peptides, 463-481, 505-523, 519-537, 603-621 and 645-663. The remaining 18 H(N) peptides had little or no inhibitory activity. In the H(C) domain, peptides 1065-1083, 1163-1181 and 1275-1296 had the highest inhibitory activities (between 25% and 29%), followed (10-12% inhibitory activity) by peptides 1107-1125, 1191-1209 and 1233-1251. Two other peptides, 1079-1097 and 1177-1195, had very low (5.8% and 4.9%) inhibitory activities. The remaining 23 H(C) peptides had no inhibitory activity. Inhibition with mixtures of equimolar quantities of the most active 6 peptides of HN, 5 of H(C) or all 11 of H(N) and H(C) revealed that the peptides contain independent non-competing binding regions. Comparison of the locations of the snp-binding regions on the H-subunit with the regions that bind blocking mouse anti-BoNT/A Abs helped explain the protecting ability of these Abs. In the three-dimensional structure of BoNT/A, the snp-binding regions that completely coincide or significantly overlap with the antigenic regions occupy surface locations and most of them reside in the last half of the H(C) domain. But some of the regions reside in the HN domain and might play a role in the translocation event.