Glucosinolates (GLSs) are abundant in cruciferous vegetables and reported to have anti thyroidal effects. Four GLSs (sinigrin, progoitrin, glucoerucin, and glucotropaeolin) were administered orally to rats, and the breakdown products of GLSs (GLS-BPs: thiocyanate ions, cyanide ions, organic isothiocyanates, organic nitriles, and organic thiocyanates) were measured in serum. Thiocyanate ions were measured by colorimetric method, and cyanide ions were measured with CI-GC-MS. Organic isothiocyanates and their metabolites were measured with the cyclocondensation assay. Organic nitriles and organic thiocyanates were measured with EI-GC-MS. In all treatment groups except for progoitrin, thiocyanate ions were the highest among the five GLS-BPs. In the progoitrin treated group, a high concentration of organic isothiocyanates (goitrin) was detected. In the glucoerucin treated group, a relatively low amount of goitrogenic substances was observed. The metabolism to thiocyanate ions happened within five hours of the administration, and the distribution of GLSs varied with the side chain. GLSs with side chains that can form stable carbocation seemed to facilitate the degradation reaction and produce a large amount of goitrogenic thiocyanate ions. Because goitrogenic metabolites can be formed without myrosinase, the inactivation of myrosinase during cooking would have no effect on the anti-nutritional effect of GLSs in cruciferous vegetables.