Abstract The assay for the carboxyterminal telopeptide of type I collagen, ICTP, has been shown to be a reliable marker in many pathological conditions but insensitive to changes in physiological bone turnover. This has induced uncertainty and confusion regarding the role of ICTP assay in the study of collagen metabolism in bones. Especially, since another assay for the carboxyterminal telopeptide of type I collagen, serum CrossLaps ELISA, sensitively follows the changes in physiological bone turnover. To find out the reasons for the discrepancy we characterized the antigenic determinant of the ICTP assay by comparing human and bovine antigens after trypsin and chymotrypsin treatments. An assay for bovine ICTP was developed contemporarily with the present study. The epitope lies on the phenylalanine rich region of two telopeptide chains. We were able to show that the region is destroyed by cathepsin K, an osteoclastic enzyme responsible for physiological bone turnover, but not by several matrix metalloproteinases (MMPs), which are important collagen degrading enzymes in pathological conditions. Cathepsin K treatment had no effect on the CrossLaps assay. The CrossLaps assay is also able to measure the MMP-derived fragments, but usually their amount is so low in serum that it is masked by the cathepsin K-derived collagen degradation. The results explain the apparent discrepancy regarding the different behaviour of ICTP and CrossLaps assays in various conditions as also verified in our study with rheumatoid arthritis patients. The ICTP assay was also found to measure only trivalently cross-linked forms of the carboxyterminal telopeptide which contains two telopeptide chains, and is therefore unable to react with divalently or histidinohydroxylysinonorleucine (HHL)-cross-linked forms of the carboxyterminal telopeptide. These forms can be measured with the SP4 (synthetic peptide 4) assay. We utilized this property in analyzing the skin samples of 18 breast cancer patients on both the irradiated and unirradiated side. The content of HHL was increased on the irradiated side, as were type I collagen synthesis and degradation. In conclusion, there are two assays for two different degradation products of the trivalently cross-linked carboxyterminal telopeptide of type I collagen, ICTP and CrossLaps, the former measuring the MMP-derived and the latter the cathepsin K-derived collagen degradation.