MOTIVATION: Zebrafish is a model organism with the ability to regenerate many different organs. Although RNA-Seq has been used extensively to study this process, there are no databases that allow easy access to data. RESULTS: Here we develop the first regeneration database that provides easy access to a large number of RNA-Seq datasets through custom-made plots of expression levels, differential expression analyses, correlations of genes and comparisons of the different datasets. zfRegeneration has a user-friendly web interface designed to enhance regeneration studies and to overcome the barriers between different research groups that study the regeneration of distinct organs. Using several case studies, we demonstrate that zfRegeneration provides a unique platform to analyse and understand gene expression during regeneration. AVAILABILITY AND IMPLEMENTATION: zfRegeneration is freely available at www.zfregeneration.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.