A new mechanism, stimulating the precipitation of calcite, is postulated. The supersaturation with respect to carbonate minerals is changed, as a result of CO2 consumption by chemolithoautotrophic, hydrogen-oxidizing bacteria. This mechanism controls the growth of atypical, microcrystalline cave pisoids in Perlová Cave, in Slovakia. The pisoids grow under calm conditions in rimstone pools, where they are bathed continuously in stagnant water. The water is supersaturated, with respect to calcite and aragonite. The bacteria inhabit the outer parts of the pisoids, covered by biofilms. The biofilm influences the supply of the Ca2+ ion, slows down the precipitation rate, and favors calcite precipitation over that of aragonite. The calcite initially precipitates as bacterial replicas, which further act as seeds for the growing calcite crystals. This process leads to the obliteration of the primary, bacterial fabrics. Since hydrogen-oxidizing bacteria occur in a wide spectrum of natural habitats, the mechanism of calcification, postulated above, also may operate in other environments.