Collagens represent a large family of structurally related proteins containing a unique triple-helical structure. Among them, the fibril-forming collagens are the most abundant in vertebrates providing tissues with form and stability. One of the characteristics of the fibrillar collagens is its sequential posttranslational modifications of specific lysine residues that have major effects on molecular assembly and stability of the fibrils in the extracellular space. Hydroxylation of lysine residues is the first modification catalyzed by lysyl hydroxylases, and is critical for the following glycosylation and in determining the fate of covalent cross-linking. This chapter presents an overview of lysine hydroxylation and cross-linking of collagen, and the analytical methods we have developed.