Background: 'There is a high level of scientific uncertainty in nanoparticle research' is often stated in the scientific literature, e.g., concerning the environmental fate of nanoparticles. Knowing more about these uncertainties and the communication about it in scientific literature and mass media might be of interest to other scientists and experts. Due to this, we compare the current state of scientific knowledge about scientific uncertainty through the example of environmental nanoparticle research with the media coverage in the field of nanotechnologies. Results: In research and review papers, scientific uncertainties, sources, and consequences are mentioned with different foci and to a different extent. In research papers, the authors focus on the certainty of specific results, whereas in review papers, the uncertainties due to a general lack of data are emphasized and the sources and consequences are discussed. The content analysis of the media coverage shows that nanotechnology is often framed as rather certain, and only one-third of the reports deal with scientific uncertainties. Furthermore, there is a strong relationship between the representations of scientific uncertainty and risks. Environmental issues are seldom mentioned.