Recent studies using germ-free mice have demonstrated that microbiota have functional roles in host homeostasis1,2. However, the phylogenetic distance between rodents and humans translates into differences in their metabolism, immune response, neural function and microbiota colonisation abilities. Hence, translational research using nonhuman primates (NHPs) is important for bridging the gap between rodent studies and human medicine3. Although several attempts to produce germ-free NHPs were made more than 50 years ago4,5, currently none are available. Here, we generated germ-free common marmosets suitable for rearing and handling under sterile conditions and maintained them with no culturable bacteria/fungi, for 22 months. The faecal microbiota composition and metabolome in conventional marmosets are more similar to those in humans than to those in mice. The transplantation of a bacterial consortium isolated from humans6 into marmosets and mice resulted in a significantly steadier bacterial colonisation in the former than that in the latter. Germ-free marmosets exhibited low levels of faecal short-chain fatty acids, bile acid metabolites, plasma and faecal immunoglobulins, and enlarged caecum in contrast-enhanced X-ray. These stable germ-free marmosets can serve as novel models that enable the development of therapeutics that target gut microbiota and elucidation of their interaction with higher-order brain function.