Soil has traditionally been distinguished from underlying saprolite, a division that has often been rationalized by the depth of biotic activity. Though numbers of roots and individual organisms in the upper 0.1 or 1.5 meter of soil generally constitute an impressive and overwhelming fraction of estimated totals, many organisms inhabit the saprolite and their accumulated effects are increasingly recognized as being substantial and formative. In this review, we examine the biological imprint on saprolite's gas, liquid, and solid phases. Evidence for biologic activity in the gas-phase of the saprolite is given by depth-dependent concentration patterns of CO2, O2, and CH4, concentration patterns that can be seasonal and that indicate biotic production and consumption of these important gases well into the saprolite. Liquid-phase evidence comes from water depletion from well drained saprolites, the presence of plant roots within saprolite, and the chemistry of soil-drainage waters. Saprolite water chemistry demonstrates a production of biogenic acids (H2CO3 and H2SO4) that can affect mineral dissolution, desilication, and element translocation and loss. Solid-phase evidence is numerous in that the saprolite in Oxisols and Ultisols can be extremely weathered and acidic environments, and due to long-continued, biologically mediated weathering, root uptake, and leaching removal of weathering products. Mass-balance methods indexed to densities and immobile elements, indicate that weathering in saprolites can lead to physical collapse or dilation, both mediated in part by biotic process. Clearly, the saprolite is often well inhabited by flora and fauna, and inventories of microbial populations indicate remarkable numbers and probable diversity of both fungi and bacteria. If soil depth is defined by the depth of organismal activity, the well-worn division of soil and saprolite is artificial and misleading. Based on biology alone, saprolite can be characterized as material that affected by pedogenesis, and considered an integral part of the soil system.