ChIPpeakAnno is a Bioconductor package designed for batch annotation of ChIP-seq and ChIP-chip data. It allows users to annotate enriched genomic regions from various experiments, including ChIP-seq, ChIP-chip, and CAGE. The package provides functionalities for visualizing binding sites as tables, pie charts, or histograms, and for determining the significance of overlaps between replicates or transcription factors. It also enables retrieval of sequences flanking binding sites for PCR, cloning, or motif discovery, and identification of Gene Ontology (GO) terms associated with adjacent genes. ChIPpeakAnno integrates with the biomaRt package for up-to-date annotation retrieval from BioMart. It supports various annotation sources, including Ensembl, UCSC genome database, and user-provided data. The package is flexible, allowing users to pass their own annotation data or existing annotation packages. It includes tools for generating Venn diagrams to visualize overlaps between datasets and for performing hypergeometric tests to assess the significance of overlaps. ChIPpeakAnno is available in Bioconductor and is compatible with R, providing a comprehensive set of tools for analyzing high-throughput sequencing data. The package is user-friendly, with functions that enable quick annotation of peaks and analysis of genomic features. It has been tested on multiple operating systems and is widely applicable across different species and experimental conditions. The package includes examples demonstrating its use in identifying binding sites, analyzing GO terms, and generating visualizations. ChIPpeakAnno is an open-source software package under the GNU General Public Licence v2.0, and its source code and documentation are available for download from Bioconductor.ChIPpeakAnno is a Bioconductor package designed for batch annotation of ChIP-seq and ChIP-chip data. It allows users to annotate enriched genomic regions from various experiments, including ChIP-seq, ChIP-chip, and CAGE. The package provides functionalities for visualizing binding sites as tables, pie charts, or histograms, and for determining the significance of overlaps between replicates or transcription factors. It also enables retrieval of sequences flanking binding sites for PCR, cloning, or motif discovery, and identification of Gene Ontology (GO) terms associated with adjacent genes. ChIPpeakAnno integrates with the biomaRt package for up-to-date annotation retrieval from BioMart. It supports various annotation sources, including Ensembl, UCSC genome database, and user-provided data. The package is flexible, allowing users to pass their own annotation data or existing annotation packages. It includes tools for generating Venn diagrams to visualize overlaps between datasets and for performing hypergeometric tests to assess the significance of overlaps. ChIPpeakAnno is available in Bioconductor and is compatible with R, providing a comprehensive set of tools for analyzing high-throughput sequencing data. The package is user-friendly, with functions that enable quick annotation of peaks and analysis of genomic features. It has been tested on multiple operating systems and is widely applicable across different species and experimental conditions. The package includes examples demonstrating its use in identifying binding sites, analyzing GO terms, and generating visualizations. ChIPpeakAnno is an open-source software package under the GNU General Public Licence v2.0, and its source code and documentation are available for download from Bioconductor.