ChIPpeakAnno is a Bioconductor package designed to facilitate the batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, or CAGE experiments. It allows users to annotate binding sites with various annotation sources, including Ensembl, UCSC genome database, and custom annotation data. The package provides functionalities for visualizing binding sites as tables, pie charts, or histograms, determining the significance of overlap between replicates or transcription factors, and retrieving sequences flanking binding sites for further analysis. It also includes tools for Gene Ontology (GO) enrichment testing and Venn diagram visualization. ChIPpeakAnno is implemented in R, leveraging the statistical environment and integration with other Bioconductor packages, such as *biomaRt* and *GOdb*. The package is flexible, user-friendly, and integrates seamlessly with other annotation and analysis tools, making it a valuable resource for researchers in genomics and bioinformatics.ChIPpeakAnno is a Bioconductor package designed to facilitate the batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, or CAGE experiments. It allows users to annotate binding sites with various annotation sources, including Ensembl, UCSC genome database, and custom annotation data. The package provides functionalities for visualizing binding sites as tables, pie charts, or histograms, determining the significance of overlap between replicates or transcription factors, and retrieving sequences flanking binding sites for further analysis. It also includes tools for Gene Ontology (GO) enrichment testing and Venn diagram visualization. ChIPpeakAnno is implemented in R, leveraging the statistical environment and integration with other Bioconductor packages, such as *biomaRt* and *GOdb*. The package is flexible, user-friendly, and integrates seamlessly with other annotation and analysis tools, making it a valuable resource for researchers in genomics and bioinformatics.