Genome-wide association studies (GWASs) have become an important tool in veterinary medicine, providing a powerful approach for identifying genomic variants associated with economically important traits in livestock. This chapter takes a closer look at the basic principles of GWASs and describes their methodology and applications in animal husbandry and disease control. GWASs play a pivotal role in improving the efficiency of animal breeding programs through genetic parameter estimation by scrutinizing single nucleotide variations to identify disease-related markers. This chapter provides an in-depth analysis of the process of marker identification and genetic parameter estimation using GWAS data, with a particular focus on improving production traits. The importance of GWASs in livestock disease management is also highlighted by emphasizing the identification of genetic variants associated with susceptibility or resistance to specific diseases. This chapter highlights the practical impact of GWASs on livestock health and productivity and their contribution to food security and sustainability. Despite these achievements, GWASs face challenges, including the need for large sample sizes and consideration of population structure and environmental factors. This chapter explores the potential of integrating GWASs with other omics technologies and concludes by highlighting the innovative capacity of GWASs to reshape livestock husbandry and disease management practices by investigating missense non-synonymous single nucleotide polymorphisms (nsSNPs)/variants in protein structures.