Microcodium is a problematic calcitic microfeature of many calcretes and calcareous paleosols in the Cretaceous and Tertiary continental and marine successions of the peri-Tethyan realm. The main controversy about the Microcodium structures is their origin and possible relation with calcified plant roots. Microcodium and rhizogenic (root-formed) microfabrics were studied in calcrete profiles within the Paleocene shallow-marine carbonate succession in southwestern Slovenia. The prominent laminar calcrete horizons contain abundant calcite aggregates, 150 μm to 1 cm in size, with perfectly preserved structural details of plant root tissues. Morphology and structure of these aggregates indicate that they formed through biologically controlled precipitation of calcium carbonate within the root cortical cells. The morphologies intermediate between the typical Microcodium aggregates, composed of a single layer of individual, elongate pyramidal or prismatic crystals of calcite (measuring 100-500 μm in length and 20-70 μm in width) and calcified roots with multilayer arrangement of isodiametric cells were observed, and this supports previous rhizogenic interpretations of Microcodium structures. Intermediate forms show that the typical Microcodium aggregates formed through morphological transformation of the root tissue by growth of the calcite within the cortical cells, which distorted the cell shape. Calcification of roots and the creation of Microcodium structures can be explained as an effective nutrient-acquiring mechanism used by certain types of terrestrial plants inhabiting nutrient-poor calcareous substrates. The widespread occurrence of Microcodium in almost unaltered shallow-marine limestones indicates that its formation took place during early stages of paleosol development, probably reflecting specific types of vascular plants of a pioneer community that were able to colonize carbonate substrates during the early phases of subaerial exposure.