BioDataome is a database of uniformly preprocessed and disease-annotated genomic and epigenomic data with the aim to promote and accelerate the reuse of public data. We followed the same preprocessing pipeline for each biological mart (microarray gene expression, RNASeq gene expression, DNA methylation) to produce ready for downstream analysis datasets and automatically annotated them with Disease-Ontology terms. We also designate datasets that share common samples and automatically discover control samples in case-control studies. Currently, BioDataome includes 6377 datasets, 301316 samples spanning 815 diseases and can be easily used in large scale massive experiments and meta-analysis. All datasets are publicly available for querying and downloading.