Clostridium botulinum neurotoxin (NT) serotypes A, B, and E have 9, 10, and 8 Cys residues, respectively, as deduced from nucleotide sequences [Whelan et al. (1992), Appl. Environ. Microbiol. 48, 2345–2354]. Each of the 150-kDa NTs has at least one disulfide; but type B, like types A and E, may have two disulfides. Using two different chemical reagents, we studied the status of the Cys residues in these three proteins after (i) the final anion exchange chromatographic step in their purification (fresh NT), (ii) 24 hr storage at 8°C, (iii) precipitation with ammonium sulfate (precipitated NT), and (iv) dissolving the precipitated NT in 6 M guanidine·HCl. In all three NT serotypes the number of Cys residues titrated with 5,5′-dithiobis-2-nitrobenzoic acid (DTNB) as free –SH groups varied, depending upon the absence or presence of EDTA added to the chromatography buffer, storage condition, age, and presence of the denaturant. Titration of 9.5–10 and 5.4–6.0 –SH groups in fresh NTs type B and E, respectively, indicated total and partial absence of disulfide bonds. Fewer titratable –SH groups in the precipitated NT than in the fresh NT suggested formation of disulfide and/or inaccessibility of the –SH groups due to protein's conformational change(s). When the precipitated NTs were dissolved in 6 M guanidine·HCl, in the absence of any added reducing agent, all Cys residues of types B and E, and 6.4–8.3 Cys in type A NT were titratable with DTNB. Iodoacetamide modification of precipitated NT types A, B, and E carboxymethylated 4, 2, and 2 Cys residues, respectively; these numbers rose to 6, 9.4, and 8 when these proteins were carboxymethylated after dissolving in 6 M guanidine·HCl in the absence of any added reducing agent. We propose that –S–S– cleavage mediated by the –SH/–S–S– exchange observed in vitro after unfolding the NTs (also unfolded by 2 M guanidine·HCl or urea) possibly mimicks a similar exchange process inside the endosomes, where the NTs are thought to undergo conformational changes, resulting in the reductive cleavage of the interchain disulfide between the 50-kDa light and 100-kDa heavy chain, which in turn releases the light chain and allows its egress out of the endosomes into the cytosol.