This chapter reviews the general biogeochemical principles underlying the use of various protein and amino acid diagenetic processes as a means of assigning relative and chronometric ages to various sample materials including bone, shell and teeth. The focus of this discussion is on racemization and epimerization processes and their application to archaeological materials and related Quaternary geological, climatic, or environmental contexts. The factors influencing accuracy and precision of the age estimates based on the measurement of the rates of amino acid racemization and modeling of factors influencing these rates are discussed.