OrganoidMap database This dataset provides a structured overview of 738 peer-reviewed original research studies employing cerebral organoids and related three-dimensional (3D) brain organoid models across neuroscience. Studies published between 1 January 2014 and 9 October 2024 were identified through a systematic literature review of PubMed, Semantic Scholar and OpenAlex conducted in accordance with PRISMA 2020 guidelines. Each row corresponds to a single study and includes standardized metadata covering neuroscience domain (neurodevelopment, neurodegeneration or neuro-oncology), disease context, organoid model type, brain region specification, cell source, species, experimental application, and reported or inferred advantages and limitations relevant to translational use. The dataset underpins the OrganoidMap web application (https://organoidmap.cs.uni-tuebingen.de) and is intended to support transparent model comparison, informed model selection and identification of underexplored areas, with particular relevance for translational neuro-oncology and brain-targeted drug development.