Abstract: Ciliates are an ancient and highly diverse group of unicellular eukaryotes that hold significant value in various fields of research such as ecology, evolutionary biology, and epigenetics. With the advancement of sequencing technology and deeper research into ciliates, an increasing amount of omics data have been generated. Here we compiled high-throughput sequencing data from 96 functional gene knockdown or knockout experiments in three genetically manipulable model ciliates, Tetrahymena thermophila, Paramecium tetraurelia, and Oxytricha trifallax, as well as other omics data from 69 ciliate species, to establish a functional genomics database for ciliates (CiliateBase; available at http://ciliatebase.maolab.org/). CiliateBase integrates various data types, including RNA-seq, ChIP-seq, MNase-seq, and RIP-seq, to analyze the functional genes and regulatory networks in ciliates. It provides tools for gene expression analysis, Gene Ontology (GO) enrichment analysis, and KEGG pathway enrichment analysis. With its user-friendly interface and powerful data visualization tools, CiliateBase enables researchers to easily search and analyze functional genomics data. It also supports downloading raw data and processed results, significantly facilitating the progress of ciliate research. In summary, CiliateBase provides a robust resource for functional genomics studies of ciliates.