Our long-term goal is to examine the role of viruses in shaping the microbial community structure and function of the gut microbiome of healthy individuals. As a microbial community, the gut microbiome is likely influenced by phages, however, little is known about their role in the human gut microbial ecosystem. Current understanding of human gut viral communities emphasizes the high level of heterogeneity found between individuals. To better estimate and identify the shared microbiome-associated viruses of healthy humans, we analyzed a deep DNA sequence dataset of active viruses and available metagenomic datasets of human gut bacteriophages communities from healthy individuals. Our first approach was direct assembly of full-length viral genomes, which revealed 23 shared viruses in more than half of 64 healthy individuals from around the world. A network analysis, similar to our assembly approach, identified 44 viral groups of which 10 (23%) were shared in more than half of all 64 individuals. These results provide strong evidence of a healthy gut virome (HGV) in humans, composed of core and common viruses present in the intestinal tract of the of healthy adult individuals and is globally distributed. Additionally, the HGV is significantly decreased in individuals with gastrointestinal disease (ulcerative colitis and Crohn’s disease). We posit that the HGV plays a critical role in maintaining the proper function of the healthy gut microbiome. Together, these results reveal a large community of human gut viruses that likely contribute to maintaining human health.