Collagens represent a large family of structurally related extracellular matrix proteins containing unique triple helical structure. One of the characteristics of this structural protein is its extensive post-translational modifications that have major effects on molecular assembly, stability, and metabolism. Hydroxylation of specific lysine residues is one of such unique modifications found in collagen, and the pattern/extent of this modification influences fibrillogenesis, cross-linking, and matrix mineralization. The formation of covalent intermolecular cross-linking is the final modification in collagen biosynthesis and is critical for the stability of collagen. The process of cross-linking is dynamic and the pathways vary depending on the tissues and tissue's physiological state. This tissue specificity of cross-linking pattern may in part be the results of differential expression of various isoforms of lysyl hydroxylases and lysyl oxidases that have been recently identified and partially characterized. This chapter concentrates on recent research progress on these two modifications and the methods for analysis we have developed.