GWASpro is a high-performance web server for the analyses of large-scale genome-wide association studies (GWASs). The server was developed to tackle challenges related to large-scale data, complex experimental designs, and steep learning curves related to existing GWAS software tools. Applications of linear mixed models for GWASs require incorporating information from experimental designs using design matrices. GWASpro supports both simple and complex design matrices for experimental designs that include replicates, treatments, and multiple environments such as multiple geographic locations and times. GWASpro is optimized to handle large-scale GWAS data, consisting of millions of markers and tens of thousands of individuals. GWASpro provides an intuitive, user-friendly interface that minimizes the learning curve.