Quality control of laboratory animals has been mostly concentrated on eliminating and securing the absence of specific infections, but event barrier bred laboratory animals harbour a huge number of gut bacteria. There is scientific evidence that the nature of the gut microbiota especially in early life - has an impact on the maturation of the immune system and thereby on the development of inflammatory deseases. In several studies, the prevalence of diseases such as rheumatic arthititis (RA), allergies, inflammatory bowel disease (IBD) an type 1 diabetes (T1D) has been shown to be positively correlated to factors related to early exposure to microorganisms, e.g. the so-called hygiene hypothesis claims that the increasing human incidence of allergy. T1D, RA and IBD may be due to the lack of such exposure. It is possible today by various molecular techniques to profile the gut microbiota of a laboratory animal, and such techniques should be applied to document uniform animals from laboratory animal vendors to secure standardization and thereby lower variation and smaller group sizes.