Grain characteristics (hardness, protein content/quality, starch properties, enzymatic activity, etc.) play an important role in the definition of end use quality for wheat-based products. Among them, gluten strength and extensibility, mostly determined by glutenin and gliadin composition, are two of the main factors that determine gluten quality. The complex inheritance of most quality traits has led to the development of indirect tests used in breeding for early and advanced generation selection. The main focus of breeders is adding resistance to biotic stress (fungi, insects, nematodes, etc.) and increasing grain yield while selection for quality often occurs in later generations. This often results in the propagation of poor quality lines that must be later discarded. Evaluation of quality in early generations requires suitable tests, preferably non-destructive. Increasing knowledge of the genes involved in quality will facilitate more precise and effective selection. Recent advances in wheat genome sequencing and the extensive genotyping of mapping populations has led to a precise molecular characterization of high molecular weight (HMW) and low molecular weight (LMW) glutenins, as well as the discovery of genes associated with quality traits like grain hardness, starch composition (e.g., waxy genes), etc. Massive genomic data will impact in breeding programs allowing quality fine tuning by precise selection of glutenins, starch, hardness and other traits, for specific end uses through marker assisted selection, genomic selection, etc. This chapter will describe different methods used for quality selection in breeding programs and research, and some examples of integration of local breeding programs with the extremely diverse end-uses of wheat based on a series of case-studies. Current and potential approaches to quality evaluation in durum wheat, wild relatives and synthetic wheat breeding programs will be also presented.