The four-domain structure of botulinum neurotoxins (BoNTs) reflects their multistep intoxication process. The high toxicity of BoNTs primarily results from specific binding and uptake into neurons mediated by their 50-kDa cell-binding fragment (HC). X-ray crystallography data have revealed that the HC fragment consists of two domains of equal size, named the 25-kDa N-terminal half of HC (HCN) and the 25-kDa C-terminal half of HC (HCC). In recent years, the ganglioside-binding sites of all seven BoNT serotypes have been allocated to the HCC domain. For BoNT/A, BoNT/B and BoNT/G, the protein receptor-binding site has been also been localized to the HCC domain. Here, we demonstrate that the HCC serotype can modulate the affinity of the HC fragment for neuronal membranes as well as the potency of full-length BoNT by replacing the BoNT/A HCC domain with the BoNT/B HCC, BoNT/C HCC and BoNT/E HCC domains, which exhibit higher affinity for synaptosomes. Indeed, the hybrids HCAB and HCAC display a higher affinity than wild-type HCA. Furthermore, the potency of a BoNT/A-based full-length hybrid containing the HCCB domain (AAAB; letters represent the serotype origin of the four domains) was quadrupled as compared with wild-type BoNT/A. Analogously, exchange of the HC fragment (AABB) yielded a neurotoxin with four-fold higher potency. As BoNT/A and BoNT/B are extensively used to treat neurological disorders, thereby facing the problem of BoNT neutralizing antibody formation, a BoNT with increased potency would lower the repeatedly administered protein dosage while maintaining the clinical benefit. Such a lowered protein load will delay the onset of neurotoxin antibody formation in patients.