Upper Pennsylvanian cyclothems of western Nebraska and southeastern Utah contain abundant brachiopods and crinoids replaced by red quartzine (length-slow chalcedony). Red fossils typically occur within silty wackestones that were deposited below fair-weather wave base during eustatic high stands. Within the "D" zone cyclothem of the Lansing-Kansas City Group (Nebraska), a well-documented paleosol recording an episode of subaerial exposure lies several meters above the chert-bearing rocks. The upper member of the Hermosa Formation (Utah) contains large-scale cross-stratified eolianites resting directly upon three red-chert-bearing limestones. Petrographic study of the silicified fossils from these two sequences shows that although fossils are presently hematitic, iron was initially concentrated within the skeletal material as scattered pyrite framboids and euhedra. Anaerobic decay of the organic material within shells during their replacement by quartzine may have led to the precipitation of pyrite. During a subsequent event, acid generated by the oxidation of pyrite inclusions allowed migration of dissolved iron through the quartzine. Buffering of these solutions by surrounding, unreplaced skeletal material caused preferential accumulation of iron oxide at the perimeters of the silicified zones. Silicification, pyrite precipitation, and pyrite oxidation all predated the crushing of shells during mechanical compaction of the matrix. We hypothesize that oxidation took place when the regional groundwater table dropped as the sea regressed and overlying beds were subaerially exposed. Cherts with similar histories should be present in other strata that bear internal sources of silica, iron, and organic material, and record large-scale, rapid changes of sea level.