In the last few years, advances in high-throughput technologies are generating large amounts of biological data that require analysis and interpretation. Nonnegative matrix factorization (NMF) has been established as a very effective method to reveal information about the complex latent relationships in experimental data sets. Using this method as part of the exploratory data analysis, workflow would certainly help in the process of interpreting and understanding the complex biology mechanisms that are underlying experimental data. We have developed bioNMF, a web-based tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications in biology. This online tool provides a user-friendly interface, combined with a computational efficient parallel implementation of the NMF methods to explore the data in different analysis scenarios. In addition to the online access, bioNMF also provides the same functionality included in the website as a public web services interface, enabling users with more computer expertise to launch jobs into bioNMF server from their own scripts and workflows. bioNMF application is freely available at http://bionmf.dacya.ucm.es.