The formation of discrete and organized inorganic crystalline structures within macromolecular extracellular matrices is a widespread biological phenomenon generally referred to as biomineralization. Recently, bacteria have been implicated as factors in biogeochemical cycles for formation of many minerals in aqueous sediments. We have found nanobacterial culture systems that allow for reproducible production of apatite calcification in vitro. Depending on the culture conditions, tiny nanocolloid-sized particles covered with apatite, forming various size of aggregates and stones were observed. In this study, we detected the presence of nanobacteria in demineralized trilobit fossil, geode, apatite, and calcite stones by immunofluorescence staining. Amethyst and other quartz stones, and chalk gave negative results. Microorganisms are capable of depositing apatite outside the thermodynamic equilibrium in sea water. We bring now evidence that this occurs in the human body as well. Previously, only struvite kidney stones composed of magnesium ammonium phosphate and small amounts of apatite have been regarded as bacteria related. 90 percent of demineralized human kidney stones now screened, contained nanobacteria. At least three different distribution patterns of nanobacteria were conditions, and human kidney stones that are formed from small apatite units. Prerequisites for the formation of kidney stones are the supersaturation of urine and presence of nidi for crystallization. Nanobacteria are important nidi and their presence might be of special interest in space flights where supersaturation of urine is present due to the loss of bone. Furthermore, we bring evidence that nanobacteria may act as crystallization nidi for the formation of biogenic apatite structures in tissue calcification found in e.g., atherosclerotic plaques, extensive metastatic and tumoral calcification, acute periarthritis, malacoplakia, and malignant diseases. In nanaobacteria-infected fibroblasts, electron microscopy revealed intra- and extra-cellular needle-like crystal deposits, which were stainable with von Kossa stain and resemble calcospherules found in pathological calcification. Thus bacteria-mediated apatite formation takes place in aqueous environments, in humans and in geological sediments.