Folding of recombinant human insulin-like growth factor-I (IGF-I) results in two distinct species as resolved by reversed-phase high-performance liquid chromatography (RP-HPLC). The earlier eluting peak (PI) has a nonnative disulfide structure, while the later eluting peak (PII) assumes the native disulfide structure. This folding problem causes a lower yield and requires expensive RP-HPLC separation. In contrast, IGF-II folds mainly into a single form with all three disulfide bonds correctly formed. Sequence comparison of the two molecules revealed that IGF-I has arginine at residues 55 and 56, while IGF-II has alanine and leucine, respectively, at these positions. Two analogs of IGF-I, IGF-I (Ala55/Leu56) and IGF-I (Leu56), behave similarly to IGF-II upon refolding and RP-HPLC; that is, a single peak eluted from the RP-HPLC column. However, when the peaks isolated by RP-HPLC were subjected to hydrophobic interaction chromatography, circular dichroism, and peptide mapping, they were found to be a mixture of PI and PII. It was then concluded that factors other than just these two residues contribute to correct folding of IGF-II and that the PI and PII of the above two IGF-I mutants assume different conformation at neutral pH but similar conformation under the RP-HPLC condition.