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Motivation Genotype imputation is essential for genome-wide association studies (GWAS) to retrieve information of untyped variants and facilitate comparability across studies. However, there is a lack of automated pipelines that perform all required processing steps prior to and following imputation. Results Based on widely used and freely available tools, we have developed Gimpute, an automated processing and imputation pipeline for genome-wide association data. Gimpute includes processing steps for genotype liftOver, quality control, population outlier detection, haplotype pre-phasing, imputation, post imputation, data management and the extension to other existing pipeline. Availability and implementation The Gimpute package is an open source R package and is freely available at https://github.com/transbioZI/Gimpute. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]