To understand the molecular stress response in maize plants to high salt and boron (B) stress, we focused on the transcript accumulation of six stress-related genes in Lluteño maize, a sweet corn landrace from the Lluta valley (northern Chile). This landrace is tolerant to salt and B stress. A randomized complete block design with four replications was used. Seedlings of Lluteño maize and maize hybrid B73 were exposed to 150 mM NaCl and 20 ppm B in nutrient solution for 120 hrs, then root and leaf samples were collected and Na + and B content were determined. Transcript accumulation of three salt stress-related genes SOS1, NHX2 and HKT1 and three B stress-related genes BOR1, BOR2 and PIP1;2 were determined in roots and leaves of Lluteño maize using RT-PCR and real-time PCR at 3 and 96 h after treatment with 150 mM NaCl and/or 20 ppm B. The results indicated that combined salt and B stress caused changes in physiological parameters. The damage was more severe in B73 than in Lluteño maize, confirming that this landrace behaves as a plant tolerant to these stresses. Regulation of stress-related genes under combined stress was different under individual stresses. The ability of Lluteño maize to survive and thrive in soil with high salinity and B concentration is probably based on a decrease in membrane water permeability, preventing salt and B uptake from the roots through down-regulation of BOR1, BOR2 transporters and PIP1;2 aquaporin. The increased water transport is mediated by the upregulation of the PIP1;2 in leaves, allowing cellular water conservation, and the retrieval of Na + from xylem through up-regulation of HKT1;1 transporters in roots and leaves.