The current LC-MS based desmosine/isodesmosine (DES/IDS) assays may be unsatisfactory for clinical use due to lack of an appropriate internal standard or low throughput. A fast and reliable LC-MS method using a D(5)-DES as an internal standard for measuring urinary total DES/IDS was developed and validated in this study. The reportable range of this assay was 1.0 and 480.0 ng/mL. The intra- and interassay imprecision, accuracy, and recovery for quality control samples were within acceptable range (<25%). Urinary total DES/IDS level was stable at room temperature or 4 degrees C for 20 h, and for three freeze/thaw cycles. The assay was employed to measure urine samples from COPD patients and demographically matched healthy volunteers. The total urinary DES/IDS levels were approximately 3-fold higher in COPD patients compared to healthy volunteers. The suitability of using urinary free DES to estimate elastin degradation was also evaluated in a second cohort. Despite urinary free and total DES/IDS levels being highly correlated, our data suggest that urinary total DES/IDS level is a preferred biomarker for elastin degradation. These results demonstrate that the LC-MS/MS method provides sensitive, reproducible and accurate quantification of urinary total DES/IDS as a biomarker for monitoring elastin degradation in diseases such as COPD.