Bacterial viruses are amongst the most numerous biological entities within the human body. These viruses are found within regions of the body that have conventionally been considered sterile, including the blood, lymph and organs. However, the primary mechanism that bacterial viruses use to access the body remains unknown. Here we use in vitro studies to demonstrate the rapid and directional transcytosis of diverse bacteriophages across confluent cell layers originating from the gut, lung, liver, kidney and brain. Bacteriophage transcytosis across cell layers had a significant preferential directionality for apical-to-basolateral transport, with approximately 0.1% of total bacteriophage applied being transcytosed over a two hour period. Microscopy and subcellular fractionation revealed bacteriophages accessed microsomal and cytosolic compartments of the eukaryotic cell, passaging via the Golgi apparatus before being exocytosed. We posit that the human body is continually absorbing phages from the gut and transporting them throughout the epithelial cell structure and subsequently the body. From our experimental results we estimate that thirty-one billion bacteriophage particles are transcytosed from the gut into the average human body each day. The transcytosis of bacteriophage is a natural and ubiquitous process that enables direct interactions between bacteriophages and the cells, organs, and immune systems of the human body.