ABAnnotate is a Matlab-based toolbox to perform ensemble-based gene-category enrichment analysis (GCEA) on volumetric human neuroimaging data via brain-wide gene expression patterns derived from the Allen Human Brain Atlas (ABA). It applies a nonparametric method developed by Fulcher et al. (2021) using spatial autocorrelation-corrected phenotype null maps for the estimation of gene-category null ensembles. ABAnnotate was adopted from Fulcher et al.`s toolbox which was originally designed for annotation of imaging data to GeneOntology categories. The function to generate null models, along with some utility functions, were taken from the JuSpace toolbox by Dukart et al. (2021). See the GitHub repository for an introduction, an overview on integrated datasets, available analysis options, and an example use case.