Gut barrier controls the food tolerance as well as host defense against potential hazards. The gut epithelium has been extensively studied for its importance in the structure and function of gut barrier. Recently, a new concept of barrier, named gut vascular barrier (GVB) has been discovered in both mice and human. Subsequent studies identified the morphological characteristics of GVB, the involved signaling events and its association with clinical diseases. In current study, we will summarize recent breakthroughs of GVB, with particular attentions to the molecular basis of GVB dysfunction. We will perform bioinformatics analysis to compare the transcriptional profiles of endothelium between blood and lymphatic vessels, healthy and inflammatory bowel diseases (IBD), healthy and colorectal cancer in the absence or presence of liver metastasis. We will further discuss the significance of impaired GVB in associated diseases, including vascular diseases, IBD and cancer metastasis. Our study will provide insights into the new concept of gut barrier, and promote the development of new strategies toward the vascular endothelium in the management of various diseases.