Genotype imputation is a crucial technique in genome-wide association studies (GWAS), allowing geneticists to evaluate the evidence for association at genetic markers that were not directly genotyped. This method increases the power of GWAS, particularly when combining results from studies using different genotyping platforms. The technique is based on the idea that shared stretches of DNA inherited from a common ancestor can provide information about unobserved genetic variants. The review covers the history and theoretical foundations of genotype imputation, illustrates its performance through real-world gene mapping studies, and discusses its role in the era of whole genome resequencing. The authors emphasize the importance of choosing appropriate reference panels for imputation in diverse populations and provide practical considerations for implementing imputation-based analyses. They also highlight the potential of genotype imputation in meta-analyses of GWAS data and its future applications in analyzing massively parallel shotgun sequence data.Genotype imputation is a crucial technique in genome-wide association studies (GWAS), allowing geneticists to evaluate the evidence for association at genetic markers that were not directly genotyped. This method increases the power of GWAS, particularly when combining results from studies using different genotyping platforms. The technique is based on the idea that shared stretches of DNA inherited from a common ancestor can provide information about unobserved genetic variants. The review covers the history and theoretical foundations of genotype imputation, illustrates its performance through real-world gene mapping studies, and discusses its role in the era of whole genome resequencing. The authors emphasize the importance of choosing appropriate reference panels for imputation in diverse populations and provide practical considerations for implementing imputation-based analyses. They also highlight the potential of genotype imputation in meta-analyses of GWAS data and its future applications in analyzing massively parallel shotgun sequence data.