OBJECTIVE The existence of microinfections produced by bacteria of a very small size (nanobacteria) could be a risk factor for stone formation. The results of a study to detect the presence of nanobacteria in calculi are presented. METHODS 1,000 calculi (excluding struvite calculi) were analyzed by macroscopic and microscopic techniques. RESULTS Microorganisms were detected in only 5 calculi (0.5%). All these calculi had developed in cavities with low urodynamic efficacy. The microorganisms were located in the center of the calculus and the main component was calcium oxalate monohydrate or uric acid. Ammonium urate/sodium urate were frequently found to be a minor component in the center of the calculus. The only common biochemical urinary alteration observed in these patients was a urinary pH below 5.5; conventional urine cultures were always negative. CONCLUSIONS Our findings demonstrate that these bacteria can play an important role in the development of calculus by inducing the formation of heterogeneous nucleants of calcium oxalate and uric acid. According to our results, however, this mechanisms is not common and would also be associated to other lithogenic risk factors. It is important to underscore that the majority of patients suffered from stomach ulcers and/or gingivitis which are conditions that could be induced by the same type of microorganisms. Therefore, it can be deduced that similar bacterial factors might be involved in pathologies that have as yet not been related. Further studies are warranted to clearly identify these bacteria.