Objectives. Alteration in the composition of extracellular matrix has been suggested as the major factor for the development of tendinopathy and calcified tendinopathy, which has poorer clinical manifestation. This study investigated the changes of major proteoglycans and collagens in a calcified tendinopathy model and correlated the expression with the acquisition of chondrocyte phenotype, ectopic ossification and loss of matrix organization in the same model. Methods. Thirty-six rats were used. Collagenase or saline was injected into the patellar tendons of each rat. At Weeks 2, 4 and 12, samples were used for immunohistochemistry of major proteoglycans and collagens and mRNA quantification. Results. An increase in collagen type III and I expression was observed after injury at Week 2. Although their levels diminished with time, the ratio of collagen type III to collagen type I remained higher than that in healthy tendon at Week 12. The expression of biglycan, fibromodulin and aggrecan increased with time, whereas the expression of decorin was sustained from Week 2 to Week 12. The expression of major proteoglycans and collagens was observed in the tendon cells and matrix at Week 2 and became localized at the chondrocyte-like cells around the calcific deposits at Week 12. Conclusion. Sustained expression of proteoglycans and a high collagen type III/collagen type I ratio might account for poor matrix organization in calcified tendinopathy. The localization of major proteoglycans around chondro-osseous region might indicate interference of collagen assembly, which favours ectopic chondrogenesis, ossification and predisposition to tendon rupture.