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Human microbiome understanding and its relationship with health has represented a revolution in biomedicine, facilitated by the emergence of new molecular microbiology techniques. Lithiasic pathology has not been alien to this new approach to etiological knowledge. As a result of this research activity, it has been possible to elucidate the importance of the intestine-kidney axis, understood as the impact of the intestinal microbiota on nephrourinary health. In this regard the ability to use oxalate as an energy source by certain intestinal microorganisms has been used as a target form odulators of the intestinal microbiota in order to correcthyperoxaluria, both primary and secondary. However,the importance of the microbiome configuration, and its role in oxalocalcic lithiasis, transcends the existence of certain trophic networks. In particular, intestinal microbiome has the ability to promote tubular lesions resulting from oxidative stress caused by chronic low-grade inflammation, closely linked to the composition of the microbiota and the dialogue established with the immune system at the intestinal level. The importance of the urobiome, a stable microbia lstructure residing in the urinary tract, allowed to calibrate the importance of urinary microorganisms in lithiasic pathology, breaking with the paradigm of urine sterility in healthy conditions. Thus, recent studies suggest that the composition and structure of the urobiome have a crucial impact on infectious but also non-infectious lithiasis, since certain microorganisms can act as nucleants and promoters of the lithogenic process. Associated with the advances in the study of binomial microbiota and lithiasic pathology, new ways are opened for patient management, in terms of prevention and treatment, based on intervention on the microbiome. Future therapeutic arsenal, in addition to probiotics and prebiotics, will integrate consortia of different microbial groups and microbiota transplantation, both urinary and intestinal.