Biological thiols – homocysteine (Hcy), cysteine (Cys), γ-glutamylcysteine (γGluCys), glutathione (GSH), and cysteinylglycine (CysGly) – in plasma samples of cystathionine β-synthase (CBS, EC 188.8.131.52)-deficient mice were quantified using hydrophilic interaction liquid chromatography (HILIC) and fluorescence detection. Mice deficient in CBS provide a model mouse of homocystinuria, an inherited metabolic disease characterized by the abnormal accumulation of Hcy in urine and blood. For quantification, the thiols were derivatized with ammonium 7-fluoro-2,1,3-benzoxadiazole-4-sulfonate (SBD-F), followed by separation with an amide column containing a mobile phase of acetonitrile–40 mM ammonium formate buffer (pH 3.0) (75/25, v/v). The total concentrations of Hcy in the plasma samples of CBS-wild type (-WT), -heterozygous (-Hetero), and -knockout (-KO) mice were 24.7, 29.3, and 237.7 μmol/L, respectively; 236.4, 178.7, and 78.5 μmol/L for Cys; 5.80, 4.87, and 0.75 μmol/L for γGluCys; 64.6, 74.0, and 51.2 μmol/L for GSH; and 2.48, 3.98, and 0.90 μmol/L for CysGly. The concentration of Hcy was significantly increased, while Cys, γGluCys, and CysGly concentrations were significantly decreased in CBS-KO mice compared to those in CBS-WT mice. The results indicated that biological thiols other than Hcy could also be utilized for the evaluation and investigation of homocystinuria pathologies.