Fecal pellet counts are often used to assess trends in ungulate population size and habitat use. However, various factors may influence the physical decay and disappearance of pellets, where disappearance may be a result of physical decay and other factors (e.g. trampling, scattering and concealment by vegetation). Knowing pellet decay and disappearance rates in different habitats is a prerequisite to acquiring reliable information from pellet counts. We examined elk Cervus canadensis pellet decay and disappearance of individual pellets and pellet groups in six habitats in the boreal forest of northwestern Canada. We monitored 120 pellet groups deposited in May 2008 at 4, 12, 16 and 28 month intervals (i.e. the end of each of three plant growing seasons) to assess differences in physical decay and disappearance. Pellet decay and disappearance varied among habitats. In moist habitats, pellets showed little sign of decay by the end of our study, likely due to a short plant growing season. In drier, open habitat types, pellet decay was more rapid, likely due to exposure to sun and wind. By the end of our study, the percent of pellets remaining varied from a 14–82% among the sampled habitats. Pellets in moist forest habitats had the lowest decay rates but the highest disappearance rates, whereas those in dry, grassland sites had the highest decay, but the lowest disappearance rates. Our study further demonstrates that ungulate pellet decay and disappearance may differ substantially among habitats, which has important implications for the design of ungulate monitoring programs that utilize pellet counts. We conclude by recommending that fecal accumulation rate (FAR) methods are likely more appropriate in our study area than fecal standing crop (FSC) methods for estimating elk density, because FAR methods are less prone to biases associated with differential pellet decay and disappearance among habitats.