The three wheat rusts, stripe rust (caused by Puccinia striiformis f. sp. tritici), leaf rust (caused by Puccinia triticina), and stem rust (caused by Puccinia graminis f. sp. tritici), are among the most important wheat diseases causing significant yield losses worldwide. Improving rust resistance in wheat cultivars is an effective way to maintain yield under rust epidemic conditions. The identification of novel rust resistance quantitative trait loci (QTLs) along with the development of genetic markers associated with these QTLs may facilitate the development of rust resistance in wheat cultivars. Therefore, this chapter summarizes the protocols and methodologies for statistical analysis of rust resistance in segregating populations at seedling and adult plant stages to identify QTL that confer rust resistance in wheat. QTL mapping is also a prerequisite for fine mapping of the genomic regions to identify an underlying genetic cause. For breeding, molecular markers that perfectly co-segregate with a linked genetic variant facilitates marker-assisted selection.