Since the discovery that Legionella pneumophila can survive and grow within free-living amoebae, there has been an increasing number of microbial species shown to have similar relationships. These include many bacterial species, fungi, other protozoa (e.g. Cryptosporidium) and viruses. Among bacteria, mycobacteria are of particular importance because of their role in human and animal infections. This review will consider the progress made in understanding the relationships between mycobacteria and amoebae, and their consequences in terms of ecology and epidemiology.