MOTIVATION: Identification of single nucleotide polymorphisms that are associated with a phenotype in more than one study is of great scientific interest in the genome-wide association studies (GWAS) research. The empirical Bayes approach for discovering whether results have been replicated across studies was shown to be a reliable method, and close to optimal in terms of power. RESULTS: The R package repfdr provides a flexible implementation of the empirical Bayes approach for replicability analysis and meta-analysis, to be used when several studies examine the same set of null hypotheses. The usefulness of the package for the GWAS community is discussed. AVAILABILITY AND IMPLEMENTATION: The R package repfdr can be downloaded from CRAN. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.