Abstract Desmosine, a crosslinking pyridinium amino acid found in elastin, is a useful biomarker for the diagnosis of diseases related to elastin degradation, such as chronic obstructive pulmonary disease (COPD). In order to achieve the precise quantitation of this compound using isotope dilution liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) analysis, isotopically‐labeled internal standards including deuterated desmosine are required. We report herein the synthesis of multi‐deuterated desmosine (d 3–9 ) as a potential internal standard. This synthesis involves the preparation of an alkyne via a Sonogashira cross‐coupling, followed by deuterogenation of the triple bond to incorporate deuterium atoms into the substrate.