Salmon calcitonin (sCT), a 32-amino-acid peptide, is the active component in many pharmaceuticals used for the management of bone diseases. In this study, the stability of sCT in rat kidney and liver homogenates were evaluated by LC-ESI-MS, and the structures of the major degradation products were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The results show that the half life of sCT was 13.18 min in rat kidney homogenate (2.5 mg/ml, protein concentration) and 43.07 min in rat liver homogenate (2.5 mg/ml, protein concentration). MALDI-TOF MS results indicated that sCT was initially cleaved at Leu9-Gly10 and Gly10-Lys11 bonds in rat kidney homogenate in vitro, at the same time, the major degradation fragment, Lys11-Pro32-NH2 Was metabolized at the C-terminal amide by deamidation, whereas in rat liver homogenate, the initial cleavage sites were at Val8-Leu9 and His17-Lys18. The results indicated that the metabolism of sCT proceeds by initial endoproteolytic cleavage and subsequent exoproteolytic digestion.