Overcoming the complexity of cheese matrix to reliably analyze cheese composition, flavor, and ripening changes has been a challenge. Several sample isolation or fractionation methods, chemical and enzymatic assays, and instrumental methods have been developed over the decades. While some of the methods are well established standard methods, some still need to be researched and improved. This chapter reviews the chemical and instrumental methods available to determine cheese composition and monitor biochemical events (e.g., glycolysis, lipolysis, and proteolysis) during cheese ripening that lead to the formation of cheese flavor. Chemical and enzymatic methods available for analysis of cheese composition (fat, protein, lactose, salt, nitrogen content, moisture, etc.) are presented. Electrophoretic, chromatographic, and spectroscopic techniques are also reviewed in the light of their application to monitor cheese ripening and flavor compounds. Novel instrumental methods based on Fourier-transform infrared spectroscopy that are currently being researched and applied to cheese analysis are introduced.