Soil salinity is one of the major abiotic stresses affecting seed germination, crop growth and productivity. In this study, seeds of three wheat (Triticum aestiveum L.) and three barley (Hordeum vulgare L.) cultivars were treated with different concentrations of NaCl to investigate the effect of salt on seed germination physiology and metabolism through the characterization of seed germination pattern, gamma-aminobutyric acid (GABA) shunt metabolite accumulation [GABA, glutamate (Glu) and alanine (Ala)] and glutamate decarboxylase (GAD) expression using RT-PCR. A trend of decreasing germination percentage with increasing NaCl concentrations was observed. Under all salt stress treatments, data showed significant increase with positive correlation (r = 0.50–0.99) between abundance of GABA shunt metabolites and salt concentration in all wheat and barley cultivars for 5 days. Increased GABA content was associated with a small but significant increase in Ala and Glu content in all cultivars. In all NaCl treatments, the transcription of GAD in terms of RNA abundance showed a significant increase in all cultivars with positive correlation (r = 0.50–0.98). Data showed significant association between GAD RNA transcription and the response of germinating seeds to salt stress in terms of GABA shunt metabolite accumulation. The elevated expression of GAD under salinity suggests the need for elevated activity of the GAD-mediated conversion of Glu to GABA during seed germination, which provides alternative metabolic routes to the respiratory machinery, balancing carbon and nitrogen metabolism and osmolyte synthesis in germinating seeds of wheat and barley under salt stress.