Gastrointestinal viruses include acute gastroenteritis virus and enterovirus. These viruses are highly contagious and human populations are generally susceptible to them, and the viruses require only tens to hundreds of virus particles to cause infection. Digital polymerase chain reaction (dPCR) has the advantages of high sensitivity, strong anti-interference and direct quantification. It has shown its uniqueness in the detection of gastrointestinal viruses, especially for samples with low viral loads, which is a beneficial supplement to the real-time PCR technology. This article reviews and looks forward to the application of digital PCR technology in gastrointestinal virus detection.