WebGestalt is a web-based tool for functional enrichment analysis of gene sets. Since its release in 2005, it has become a popular software tool for interpreting gene lists from large-scale genetic, transcriptomic, and proteomic studies. The latest version of WebGestalt supports 8 organisms and 201 gene identifiers from various databases and platforms, providing extensive coverage of functional categories. It integrates functional categories from centrally curated databases, open collaborative platforms, and computational analyses, resulting in 78,612 functional categories. New interactive features, such as pathway maps, hierarchical network visualization, and phenotype ontology visualization, have been added to help users better understand enrichment results. The new version of WebGestalt supports a broader range of gene identifiers, including those from major high-throughput platforms for human and seven important model organisms. It also includes six types of functional categories: GO, Pathway, Network, Phenotype, Disease, Drug, and Chromosomal location. The tool has expanded its pathway collection to include data from Pathway Commons and WikiPathways, enhancing pathway coverage. Gene sets associated with diseases and drugs, inferred using GLAD4U, have been added to the tool. These gene sets have been used to demonstrate the utility of the new features, such as identifying disease terms and drug associations. WebGestalt has also introduced new visualization features, including enriched DAGs for revealing hierarchical relationships of enriched GO terms and network modules. It provides methods for visualizing input genes and their neighbors in enriched modules, as well as pathway maps from WikiPathways. The tool has added five methods for multiple-test correction of enrichment P-values and a 'Top10' feature to provide users with a quick overview of the most enriched categories. It has also removed the login requirement and provided options for downloading analysis results for archiving and sharing. The new version of WebGestalt has significantly increased the coverage of organisms, gene identifiers, and functional categories, enabling enrichment analysis against unique data sources such as the publicly curated WikiPathways database, hierarchical network modules, phenotype ontology, and disease and drug-associated gene sets. It has implemented new visualization features for presenting pathway, phenotype, and network enrichment analysis results. WebGestalt continues to be updated to support more gene identifiers and curated functional categories, develop new computational methods, and improve the user interface.WebGestalt is a web-based tool for functional enrichment analysis of gene sets. Since its release in 2005, it has become a popular software tool for interpreting gene lists from large-scale genetic, transcriptomic, and proteomic studies. The latest version of WebGestalt supports 8 organisms and 201 gene identifiers from various databases and platforms, providing extensive coverage of functional categories. It integrates functional categories from centrally curated databases, open collaborative platforms, and computational analyses, resulting in 78,612 functional categories. New interactive features, such as pathway maps, hierarchical network visualization, and phenotype ontology visualization, have been added to help users better understand enrichment results. The new version of WebGestalt supports a broader range of gene identifiers, including those from major high-throughput platforms for human and seven important model organisms. It also includes six types of functional categories: GO, Pathway, Network, Phenotype, Disease, Drug, and Chromosomal location. The tool has expanded its pathway collection to include data from Pathway Commons and WikiPathways, enhancing pathway coverage. Gene sets associated with diseases and drugs, inferred using GLAD4U, have been added to the tool. These gene sets have been used to demonstrate the utility of the new features, such as identifying disease terms and drug associations. WebGestalt has also introduced new visualization features, including enriched DAGs for revealing hierarchical relationships of enriched GO terms and network modules. It provides methods for visualizing input genes and their neighbors in enriched modules, as well as pathway maps from WikiPathways. The tool has added five methods for multiple-test correction of enrichment P-values and a 'Top10' feature to provide users with a quick overview of the most enriched categories. It has also removed the login requirement and provided options for downloading analysis results for archiving and sharing. The new version of WebGestalt has significantly increased the coverage of organisms, gene identifiers, and functional categories, enabling enrichment analysis against unique data sources such as the publicly curated WikiPathways database, hierarchical network modules, phenotype ontology, and disease and drug-associated gene sets. It has implemented new visualization features for presenting pathway, phenotype, and network enrichment analysis results. WebGestalt continues to be updated to support more gene identifiers and curated functional categories, develop new computational methods, and improve the user interface.