Problem soils have serious physical and chemical constraints, impose stress on crops under cultivation and reduce its yield and productivity. Research efforts towards the development of tolerant cultivars for problem soils have gained all the advances from research areas of genomics but precision phenotyping still remains challenging. This chapter illustrates different phenotyping methods which have been used to screen genotypes against various problem soil conditions, discusses bottlenecks in the classical methods of phenotyping and exemplifies the application of high-throughput (HT) phenotyping in the current field of interest through red, green, blue (RGB) imaging, infrared thermography, chlorophyll fluorescence and hyperspectral imaging technologies. The HT phenotyping is a useful technique, and when it is empowered with other tools such as high-density linkage mapping and association mapping, it can accelerate the breeding process. © Springer India 2015.