High-throughput phenotyping is a rapidly evolving field, with new technologies being developed that need to be tested under different experimental conditions. In this study, the PlantEye, a high-resolution three-dimensional (3D) laser scanner was used to phenotype wheat plants grown under control and salt stress in controlled environment conditions. The PlantEye scans plants from overhead, creating a data cloud from which the system computes traits such as 3D leaf area, plant height and leaf number. Moderately high correlations were observed between automatically calculated trait; 3D leaf area, and the manually measured traits leaf area, fresh biomass and dry biomass, although correlations were lower than those reported in previous studies in different crop species. As expected, salt stress caused significant reduction in plant growth, particularly leaf area and biomass production, which resulted in significantly reduced grain number and yield. The results here suggest that PlantEye was effective in phenotyping wheat, although improvements in the system setup, data processing and customer support would make this phenotyping tool suitable to be widely adopted for a range of plant species under diverse environmental conditions.