Homocysteine (Hcy), a sulfur-containing amino acid, is a representative intermediate metabolite of methionine (Met) to cysteine (Cys) via several intermediates. An elevated level of Hcy in plasma plays an important role in diseases such as neural tube defects and Down syndrome. Homocystinuria is the most common inborn error of sulfur metabolism and is caused by mutations in the metabolic enzymes of Hcy. These errors can be caused by abnormal levels of Met metabolites and classified on the basis of plasma Met levels. Additionally, Hcy and related compounds such as glutathione play an important role in maintaining homeostasis. Therefore, the simultaneous determination of Hcy and/or related compounds is required for appropriate clinical management of several diseases. The sulfur-containing amino acids and their derivatives in biological samples are quantified sensitively using high-performance liquid chromatography methods coupled with various detection methods such as UV/Vis, fluorescence, chemiluminescence, electrochemical, mass spectrometry, and tandem mass spectrometry. In this chapter, we review recent advances in these analytical methods and their applications.