Abstract: ¹³C is a stable nuclide and its labeled substrates have already used in clinic.Among the substrates, ¹³C-urea is the mainstream of clinical practice to diagnose the Helicobacter pylori.The other substrates such as aminopyrine, methacetin, octanoic and mixed triglyceride are used to diagnose diseases of the digestive system.Because the ¹³C-labeled compounds are non-invasive, safe, nonradiative and suitable for pregnant women and children, so many researchers focus on them.This paper makes a review on the research progress of ¹³C-labeled substrates in the diagnosis of digestive system disease in recent years.