Probiotics are frequently used for multiple objectives and the majority of applications are performed both in human beings and in different animals. The specificity of species showed by the members of the indigenous microbiotia led us to isolate lactic acid bacteria (LAB) from their natural bovine ecosystems and to select those with probiotic potentiality. The beneficial probiotic LAB were isolated from the vaginal tract and mammary gland of adult heifers, faeces and oral cavity of newborn calves. Bacterial strains and their numbers varied in each tract under study. Their surface properties, evaluated using the MATH test, revealed that the higher number of low hydrophobic strains were isolated from vaginal tract, mammary gland or faeces. The capability of autoaggregation also differed with higher degree in those isolated from vagina, whereas those that originated in the mammary gland or faeces showed low autoaggregation characteristics. The production of antagonistic substances showed that the production of hydrogen peroxide was higher in the strains isolated from the vaginal tract, while those able to produce organic acid were isolated from all the environments. A few strains were able to produce bacteriocins and were isolated only from the mammary gland and faeces, but not from the vaginal tract. Further studies are being performed to complete the functional characterization of the strains in order to evaluate their survival in the environmental conditions of each tract. Finally, the selected strains could be combined for the design of probiotic products to be used both in adult cows and in neonates, based on the host-specificity, due to their autochthonous origin and their potential use in the tract where they were isolated.