Recombinant human bone morphogenetic protein-2 (rhBMP-2), a cystine-knot containing disulfide-linked homodimer, was produced in form of inclusion bodies (IBs) using E. coli. BL21 (DE3) and SHuffle 17 Express. Non-reducing SDS-PAGE analysis revealed that rhBMP-2 was present within IBs in both strains as monomer and in form of disulfide-linked dimers. Purified dimeric disulfide-linked rhBMP-2 was obtained from IBs by two different methods. The first method involved classical solubilization using strong denaturants and subsequent refolding. The second method involved mild extraction without refolding. Both rhBMP-2 dimer variants were purified by Heparin-affinity chromatography. Mildly extracted rhBMP-2 was further purified by size-exclusion chromatography. The resulting dimeric rhBMP-2 variants were studied regarding bioactivity and folding status. In contrast to the rhBMP-2 dimer obtained by classical refolding it was shown that the disulfide-linked dimer obtained by mild extraction was not correctly folded e.g. the hydrophobic core not correctly formed. Moreover, refolded dimeric rhBMP-2 was bioactive and the mildly extracted dimeric rhBMP-2 did not show any bioactivity. Disulfide-bond analysis revealed that the intricate disulfide-bond pattern of the complex cystine-knot scaffold was not present in the IB embedded disulfide-linked rhBMP-2 dimer but was formed later during classical refolding of the reduced protein under appropriate redox conditions.