The recent advances made in the use of infrared thermal imaging (thermography) as a non-invasive, high-throughput technique for the screening of salinity tolerance in plants is reviewed. Taking wheat seedlings as an example, the methods and protocols used to impose a homogeneous salt stress to a large number of genotypes, as well as capturing infrared images of these genotypes and automatically processing the images are described in detail in this chapter. We also present the source code of the Matlab program applied to automatically identify plants and batch process IR images.