Gut microbiota contains tens of trillions microbes, including bacteria, archaea, fungi and viruses that resident in our intestinal tract. Extensive researches in recent years highlight that human physiology, metabolism, nutrition, immune function and central nerve system are influenced by gut microbiota. Gut microbiota dysbiosis, which refers to a profound imbalance in the intestinal microbiota, has been linked with many diseases, such as inflammatory bowel disease, obesity, type 2 diabetes, neural disorder disease and cancer. The majority of studies to date, however, have been focused on the influence of gut commensal bacteria. Recently, a growing number of evidences indicate that gut virome plays a fundamental role in our health and disease as well. The human gut virome is composed of a diverse collection of single strand or double strand, DNA or RNA viruses, such as phages that infect bacteria or archaea, eukaryotic viruses that able to replicate in human cells, food-derived plant or animal viruses, as well as endogenous retrovirus elements that integrated in our genome. As sequencing data continually accumulated, it is clear that there are huge amount of viruses harboring in human intestine. Each individual person harbors unique and dynamic gut virome. Emerging data indicate that enteric viruses regulate, and are in turn regulated by other microbes through a series of processes termed "transkingdom interactions". Despite recent rapid advances, there are still major gaps in understanding the biological function and detailed mechanism of gut virome. Although still technically challenge, more functional studies are necessary to understand how gut virome interact with host in addition to association studies. Here we summarize some of the most recent progresses on gut virome in health and disease. Meanwhile we also highlight current challenges and discuss future direction in the field.