Measurement of bat guano deposition rate in caves can be an important research tool for estimation of colony size, for monitoring the record of long-term bat population trends, and for allied studies of guano invertebrate ecology, environmental contaminants, and paleoecology. However, previously published methodologies have lacked consistency. In the context of our recent studies of insectivorous bat guano deposition rates in Deer Cave, Sarawak, Borneo, we review some past studies and offer suggestions for best practises, along with proposed experimental design considerations for future studies (e.g., design of guano catchers, optimum deployment of catchers in relation to specific site characteristics, data reporting standards, and examples of mapping techniques). Consistent techniques will facilitate inter-site comparisons, and determination of intra-site changes over time. As a case study, and the first publication of detailed mapping of spatial variability in guano deposition rates, we present spatially explicit guano deposition rates for Deer Cave, ranging up to 88 g (dry weight)/m²/day in the main cave, and up to 540 g (dry weight)/m²/day in the northern extension.