Background Current evidence indicates that increased desmosine excretion reflects the active inflammatory status of some connective tissue diseases. Our goal was to establish a reliable method of detection and to investigate the normal distribution of urinary desmosine excretion in a healthy pre-pubertal population.Method Urine was collected from healthy volunteers aged four weeks to 12 years old. We modified a published high-performance liquid chromatography (HPLC) method by (a) increasing hydrolysis time and temperature and (b) increasing cellulose column size.Results Our modified method had small inter- and intra-assay variability, with coefficients of variation of <6.4% and 5.3%, respectively. There was positive correlation between isodesmosine and desmosine (r(2) = 0.91). There was no significant diurnal or day-to-day variability in total desmosine levels. A reference range for healthy pre-pubertal children aged four weeks to 12 years was established.Conclusion The modified HPLC method is reliable with low variability. The technique can now be applied as a non-invasive research or diagnostic tool for children with chronic lung disease.