Decreases in the diversity of enteric bacterial populations are observed in patients with Crohn’s disease (CD) and ulcerative colitis (UC). Less is known about the virome in these diseases. We show that the enteric virome is abnormal in CD and UC patients. In-depth analysis of preparations enriched for free virions in the intestine revealed that CD and UC were associated with a significant expansion of Caudovirales bacteriophages. The viromes of CD and UC patients were disease and cohort specific. Importantly, it did not appear that expansion and diversification of the enteric virome was secondary to changes in bacterial populations. These data support a model in which changes in the virome may contribute to intestinal inflammation and bacterial dysbiosis. We conclude that the virome is a candidate for contributing to, or being a biomarker for, human inflammatory bowel disease and speculate that the enteric virome may play a role in other diseases. Display omitted •The enteric virome is abnormal in multiple inflammatory bowel disease patient cohorts•The enteric virome richness increases in Crohn’s disease and ulcerative colitis•Decreases in bacterial diversity and richness in IBD do not explain virome changes•Virome changes in Crohn’s disease and ulcerative colitis are disease specific The enteric virome is abnormal in multiple cohorts of inflammatory bowel disease patients, exhibiting disease-specific features that are not explained by changes in bacterial diversity and richness.