Gold nanoparticles have particular properties distinct from those of bulk gold crystals, and such nanoparticles are used in various applications in optics, catalysis, and drug delivery. Many reports on microbial synthesis of gold nanoparticles have appeared. However, the molecular details (reduction and dispersion) of such synthesis remain unclear. In the present study, we studied gold nanoparticle synthesis by Lactobacillus casei. A comparison of L. casei components before and after addition of an auric acid solution showed that the level of unsaturated lipids decreased significantly after addition. NMR and mass spectrum analysis showed that the levels of diglycosyldiacylglycerol (DGDG) and triglycosyldiacylglycerol (TGDG) bearing unsaturated fatty acids were much reduced after formation of gold nanoparticles. DGDG purified from L. casei induced the synthesis of gold nanoparticles in vitro. These results suggested that glycolipids, such as DGDG, play important roles in reducing Au(III) to Au(0) and in ensuring that the nanoparticles synthesized remain small in size. Our work will lead to the development of novel, efficient methods by which gold nanoparticles may be produced by, and accumulated within, microorganisms.