Background: Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While the corresponding raw and processed data are made available through specialized public databases, the processed files are usually limited to a specific research question. Hence, they are unsuitable for an unbiased, systematic overview of a complex dataset. However, possible combinations of different sample types and conditions grow exponentially with the amount of sample types and conditions. Therefore the risk to miss a correlation or to overrate an identified correlation should be mitigated in a complex dataset. Since reanalysis of a full study is rarely a viable option, new methods are needed to address these issues systematically, reliably, reproducibly and efficiently. Results: Cogito "COmpare annotated Genomic Intervals TOol" provides a workflow for an unbiased, structured overview and systematic analysis of complex genomic datasets consisting of different data types (e.g. RNA-seq, ChIP-seq) and conditions. Cogito is able to visualize valuable key information of genomic or epigenomic interval-based data, thereby providing a straightforward analysis approach for comparing different conditions. It supports getting an unbiased impression of a dataset and developing an appropriate analysis strategy for it. In addition to a text-based report, Cogito offers a fully customizable report as a starting point for further in-depth investigation. Conclusions: Cogito implements a novel approach to facilitate high-level overview analyses of complex datasets, and offers additional insights into the data without the need for a full, time-consuming reanalysis. The R/Bioconductor package is freely available at https://bioconductor.org/packages/release/bioc/html/Cogito.html, a comprehensive documentation with detailed descriptions and reproducible examples is included.