Seedlings of Brassica rapa were exposed to increasing concentrations of NaCl, Na2SO4, KCl and K2SO4 to study the effect on glucosinolate content, composition and expression of genes of the glucosinolate biosynthetic pathway and associated transcription factors. Growth was inhibited stronger by sulfate salts and strongest by Na2SO4. Aliphatic, indolic and aromatic glucosinolates were differently affected by the salts in shoot and roots. A decrease of aliphatic glucosinolates in shoots of plants exposed to chloride salts corresponded to a decreased gene expression of a key enzyme for their biosynthesis. Likewise, an increased level of indolic and aromatic glucosinolates by Na2SO4 coincided with an increased gene expression of enzymes responsible for the biosynthesis of these glucosinolates. The results show that changes in glucosinolate content and composition under salt stress depend on the ionic composition of the salts. This has implications for the quality of Brassica rapa grown under different types of salinity.