Thin sections of partially silicified brachiopods from the Mississippian Lodgepole Limestone show authigenic silica in contact with original calcite microstructure. No void-filling quartz morphologies are present. Of the three types of biogenic microstructures represented in the taxonomically diverse material, fibrous structure was the most susceptible to replacement, whereas laminar structure was the most resistant to silicification. This difference probably reflects the greater microporosity and reactive surface area of the fibrous structure. Skeletal microstructure was more important than valve thickness in determining extent of silicification, although there is a positive correlation between thickness and replacement in any one taxon. The lack of a uniform silicification pattern among these monomineralic taxa of different microstructure indicates that skeletal factors exerted the most significant controls on brachiopod replacement. Microstructure-controlled replacement typifies fibrous layers whereas laminar layers show microstructure-independent replacement. Prismatic structure, characteristic of an inner layer in spiriferide valves, shows the former mode of replacement in some instances and the latter mode in others. In both cases, silicificafion is most complete adjacent to the overlying fibrous layer. Microstructure-controlled replacement commonly involves anhedral or subhedral megaquartz in contrast to the fibrous quartz morphology reported by several authors for silicified brachiopods from other regions. Microstructure-independent replacement involves either spherulitic chalcedony or euhedral megaquartz. Both modes of replacement, that replicating microstructure and that crosscutting it, have been observed in different parts of a single valve.