The human gastrointestinal tract is colonized by a dense population of microorganisms, referred to as the bacterial flora. Although the gut provides a functional barrier between these organisms and the host, bacterial translocation is a common event in the healthy person. However, in critically ill patients, with various underlying diseases, this bacterial translocation may lead to infections and consequently to a further reduction in general health status. The mechanism of bacterial translocation is widely, and somehow controversially investigated in vitro and in animal models. In human studies, several diseases have been associated with bacterial translocation. However, methodological shortcomings, insufficient populations and conflicting results leave many open questions. This is also reflected in the various published therapeutic strategies. To overcome this problem more investigations in humans are needed, especially in techniques for detecting bacterial translocation.