Alkaline and alkaline earth cations have been used in the synthesis of SBA-3, a silica mesoporous materials. These cations can not substitute silicon in the silica structure. However, we found that SBA-3 surface area, pore size and thickness, periodic order, and microporosity were affected by the presence of lithium, magnesium, or calcium ions. Chemical interactions among these ions and silica species are supposed to occur on the SBA-3 pore surface.