The influence of the bacteria Bacillus subtilis (B. subtilis) on the nucleation, growth and aggregation of calcium oxalate (CaOx) crystals in aqueous solution has been studied. The crystals obtained were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy and X-ray powder diffractometry. The results show that, in the presence of B. subtilis, quasi-hexagonal calcium oxalate monohydrate (COM) crystals are obtained after 24 hours of reaction at a temperature of 30°C ± 1K. However, without the presence of the bacteria, irregular CaOx crystals were obtained which contain two crystal phases: COM and calcium oxalate dihydrate (COD). This suggests that B. subtilis may promote the crystallization of COM, the major component of urinary stone. The formation mechanism of CaOx crystals in the presence of B. subtilis is explored, indicating that the cell walls and extracellular proteins of the bacteria may act as templates to induce the nucleation, growth and aggregation of CaOx crystals.