Bacillus coagulans is a probiotic bacterium that produces spores. Due to its excellent stability, it has been widely used in medicine, food and chemical industry. Recent studies have shown that B. coagulans has therapeutic effects on intestinal diseases, such as acute diarrhoea, irritable bowel syndrome, antibiotic-related diarrhoea, constipation and colitis via modulation of the microbiota composition, host immunity and metabolism. Additionally, toxicological experiments and a large number of clinical observations have showed that B. coagulans is safe and has no effect of mutagenicity, teratogenicity or genotoxicity. This review summarises the latest advances associated with B. coagulans, from its biological features, probable action mechanisms, toxicity, and medical applications.