Ebola virus (EBOV) is a negative strand RNA virus that causes Ebola virus disease (EVD) with a high case fatality rate. During the acute phase of infection, a subsequent fatal outcome is characterized by an increased upregulation of interferon and inflammatory pathways compared to survivors. Replication of genomes from negative strand RNA viruses (and RNA viruses in general) can result in the generation of defective genomes that may interfere with viral replication and stimulation of the innate immune response. We characterized the presence of defective genomes in blood samples from humans who were positive for EBOV and processed by the European Mobile Laboratory during the 2013-2016 West African EVD outbreak. A bioinformatics tool, DI-tector, was used to identify sequence motifs associated with the four different types of defective genomes. The analysis indicated that sequence features indicative of defective genomes were present in blood samples in patients during the acute phase of infection. The most common type of defective genome identified was insertion followed by deletion, 5' copy back and then 3' copy back. In general, the abundance of defective genomes correlated with viral load, but particularly with patient outcome. We postulate that the presence of defective genomes correlates with an upregulation in the interferon response and resultant inflammation and may, therefore, be an important contributory factor in patients with severe EVD.IMPORTANCEEBOV and filoviruses in general are high consequence infectious diseases whose outbreaks can severely impact the lives of those affected. In this study, we show that during EBOV replication in humans, defective genomes can be produced, which complements previous studies in nonhuman primate models of disease and in cell culture. The abundance of these defective genomes correlates with disease outcome in acutely ill patients. In people who go on to die from EVD, they appear to have higher levels of defective genomes than in people who go on to survive infection. This may, in turn, cause a greater upregulation of interferon and inflammation, which are some of the biggest factors in determining disease severity and adverse patient outcome. Therefore, we caution the potential use of defective genomes as a therapy for EVD, as has been proposed for other negative strand RNA viruses.