The aims of the study were to characterize the denaturation of urinary free and conjugated pyridinoline (Pyr) and deoxypyridinoline (Dpyr) on exposure to ultraviolet (UV) and natural light at different pH levels and to study the effects of X- and gamma-irradiation on Pyr and Dpyr in urine and in the mineralized and non-mineralized compartments of human bone. Urine samples from six normal subjects, adjusted to pH 3.0, 7.0 and 9.0 were exposed to UV light for up to 3 days. Urine collections (2 mL and 24 h) from three subjects, pH adjusted to 1.0, 2.0, 3.0, 4.0 and 5.0, were exposed to natural light for up to 1 day. Urine samples and bone slices from seven human cadaveric femurs were irradiated with increasing doses of X-rays (0-100 Gy) and high-dose gamma-radiation (28 kGy). Mineralized and non-mineralized bone were separated using a modification of a published method employing heat denaturation followed by trypsin hydrolysis and analysed for Pyr, Dpyr and hydroxyproline (Hypro). The rate of UV photolysis of urinary Pyr and Dpyr increased with pH and was faster in the free fraction (after 3 days' exposure: free Pyr and Dpyr at pH 7.0 vs. 9.0, P < 0.05, conjugated pH 3.0 vs. 9.0, P < 0.05). Exposure to natural light for 3 h did not significantly decrease urinary Pyr and Dpyr in either sample collections, but levels were reduced in the 2-mL aliquots after exposure for 1 day (P < 0.05). X-irradiation of urine and bone did not affect Pyr and Dpyr. Pyr content was similar in both bone compartments (Pyr/ Hypro = 0.12 +/- 0.004), but Dpyr was higher in the non-mineralized compartment (Dpyr/Hypro = 0.047 +/- 0.002 vs. 0.038 +/- 0.002, P < 0.001). UV light and gamma-irradiation result in denaturation of pyridinium cross-links in urine. These cross-links are present in both the mineralized and non-mineralized bone compartments but are not affected by the doses of gamma-irradiation that denature these cross-links in urine.