A 43 cm long E271 sediment core collected near the East Pacific Rise (EPR) at 13°N were studied to investigate the origin of smectite for understanding better the geochemical behavior of hydrothermal material after deposition. E271 sediments are typical metalliferous sediments. After removal of organic matter, carbonate, biogenic opal, and Fe-Mn oxide by a series of chemical procedures, clay minerals (<2 μm) were investigated by X-ray diffraction, chemical analysis and Si isotope analysis. Due to the influence of seafloor hydrothermal activity and close to continent, the sources of clay minerals are complex. Illite, chlorite and kaolinite are suggested to be transported from either North or Central America by rivers or winds, but smectite is authigenic. It is enriched in iron, and its contents are highest in clay minerals. Data show that smectite is most likely formed by the reaction of hydrothermal Fe-oxyhydroxide with silica and seawater in metalliferous sediments. The Si that participates in this reaction may be derived from siliceous microfossils (diatoms or radiolarians), hydrothermal fluids, or detrital mineral phases. And theirδ30Si values are higher than those of authigenic smectites, which implies that a Si isotope fractionation occurs during the formation because of the selective absorption of light Si isotopes onto Fe-oxyhydroxides. Sm/Fe mass ratios (a proxy for overall REE/Fe ratio) in E271 clay minerals are lower than those in metalliferous sediments, as well as distal hydrothermal plume particles and terrigenous clay minerals. This result suggests that some REE are lost during the smectite formation, perhaps because their large ionic radii of REE scavenged by Fe-oxyhydroxides preclude substitution in either tetrahedral or octahedral lattice sites of this mineral structure, which decreases the value of metalliferous sediments as a potential resource for REE.