The increasing popularity of epigenome-wide association studies (EWAS) has led to the establishment of several large international meta-analysis consortia. However, when using data originating from multiple sources, a thorough and centralized quality control is essential. To facilitate this, we developed the QCEWAS R package. QCEWAS enables automated quality control of results files of EWAS. QCEWAS produces cohort-specific statistics and graphs to interpret the quality of the results files, graphs comparing results of multiple cohorts, as well as cleaned input files ready for meta-analysis.