The formation of mineral deposits in mesothermal quartz veins is a complex process that has been the subject of much research. The classical fault-valve hypothesis suggests that mineralization occurs when metamorphic fluids are injected during a brittle event and then locked in to mineralize, but this hypothesis does not fully explain the regular spacing of repeated mineralized patterns that are often observed. This paper proposes a new mechanism for mineralizing systems based on the theory of cnoidal waves in solids. Cnoidal waves are standing waves that can persist for long times in materials under compressive and extensional regimes. We investigate mineral deposits by analytical and numerical methods and show that the cnoidal wave instability theory provides a plausible alternative mechanism for mineralizing systems. This study opens a new avenue for field studies to demonstrate that the mechanism-based cnoidal waves play an essential role in the formation of mineral deposits.