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Biological synthesis of gold and silver nanoparticles was carried out using the bacteria Bacillus subtilis. The reduction processes of chloroaurate and silver ions by B. subtilis were found to be different. Gold nanoparticles were synthesized both intra- and extracellularly, while silver nanoparticles were exclusively formed extracellularly. The gold nanoparticles were formed after 1 day of addition of chloroaurate ions, while the silver nanoparticles were formed after 7 days. The nanoparticles were characterized by X-ray diffraction, UV-vis spectra and transmission electron spectroscopy. X-ray diffraction revealed the formation of face-centered cubic (fcc) crystalline gold nanoparticles in the supernatant, broth solution and bacterial pellet. Silver nanoparticles also exhibited diffraction peaks corresponding to fcc metallic silver. UV-vis spectra showed surface plasmon vibrations for gold and silver nanoparticles centered at 530 and 456 nm, respectively. TEM micrographs depicted the formation of gold nanoparticles intra- and extracellularly, which had an average size of 7.6 +/- 1.8 and 7.3 +/- 2.3 nm, respectively, while silver nanoparticles were exclusively formed extracellularly, with an average size of 6.1 +/- 1.6 nm. The bacterial proteins were analyzed by sodium dodecyl sulfonate-polyacrylamide electrophoresis (SDS-PAGE) before and after the addition of metal ion solutions. We believe that proteins of a molecular weight between 25 and 66 kDa could be responsible for chloroaurate ions reduction, while the formation of silver nanoparticles can be attributed to proteins of a molecular weight between 66 and 116 kDa. We also believe that the nanoparticles were stabilized by the surface-active molecules i.e., surfactin or other biomolecules released into the solution by B. subtilis.