Bioheap leaching of secondary copper ores is applied commercially at operations in Chile and Australia. Bioheap leaching of sulfidic refractory gold ores has been demonstrated at large scale. There is limited comprehension of what actually occurs microbiologically in full-scale bioheap operations, despite the commercial achievement of copper ore bioheap leaching and the anticipated technical and commercial success of gold ore bioheap leaching. Copper bioheaps are typically inoculated with the bacteria contained in the raffinate, whereas, sulfidic refractory gold ore bioheaps can be inoculated with bacteria developed in a separate reactor. Chemical and physical conditions within bioheaps change radically from the time the bioheap is stacked and inoculated until bioleaching is completed. Redox, acidity, temperature, oxygen and solution chemistry conditions can vary widely during the oxidation period. Such conditions likely select for microorganisms or may, in fact, effect a succession of organisms in portions of the bioheap. Bioheap solutions are recycled and constituent build-up over time also affects the microbiology. Heterotrophic microorganisms may also play some role in bioheap leaching. Understanding the microbiology of bioheaps is key to advancing commercial bioheap applications. Such knowledge will increase the ore types as well as the diversity of mineral deposits that can be processed by bioheap technology. It will also enable better control of conditions to improve leach rates, metal recoveries and costs. This paper briefly explains commercial practices, describes chemical, physical and microbiological monitoring of bioheap, considers conditions that control microbial populations in bioheaps, and examines the types of ore deposits that could be bioleached, if the microbiology was elucidated.