Carbonate concretions (N = 18) from the Middle Devonian Hamilton Group were studied using CT X-ray imaging and with computerized 3-D reconstructions. Pyritized burrows and/or body fossils appear causally related to these concretions. When pyritization was noted on the outside of the specimen (N = 15), corresponding networks of pyritized full relief burrow traces could be demonstrated internally. Even when not noted externally, some evidence of pyritic, full relief burrows was noted in all specimens. Because of pyrite opacity, and density contrasts between the limestone concretions and pyrite, these burrows can be tracked through serpentine pathways using 3-D techniques. A brachiopod at the nucleus of one concretion displays X-ray evidence of a possible three-dimensional pedicle preserved in pyrite. This would then be one of the few known pedicles preserved in an articulate brachiopod in the fossil record. Halo formation around the shell edge suggests decaying visceral organic tissue as a probable source of a microbial biofilm, which, in turn, could have served as the nucleus of the concretion. A sequential mechanism is proposed in which both the mucous of burrowing organisms and the decay of visceral tissue served to localize pyritic crusts and concretions near the site of decay, followed by carbonate concretionary growth as pH increased, and available sulfide and iron decreased further from the decay source. These processes comprise end-members in a diagenetic continuum, based on a gradually changing local microbial and chemical environment. Increased bioturbation in studied concretions compared with surrounding sediment suggests increased residence time within the sulfate reduction zone due to sediment starvation following initial rapid burial. This diagenetic observation is suggested to apply to many other cases of concretion formation.