Reduction of crown fire hazard in Pinus ponderosa forests in the Black Hills, SD, often focuses on the removal of overstorey trees to reduce crown bulk density. Dense ponderosa pine regeneration establishes several years after treatment and eventually increases crown fire risk if allowed to grow. Using prescribed fire to control this regeneration is hampered by the limited knowledge of fire-related mortality threshold values for seedlings (<1.4 m tall) and saplings (0.25 to 10 cm diameter at breast height). The present study was initiated to assess fire-related mortality of ponderosa pine seedlings and saplings on prescribed burns across the Black Hills. We established plots in several burn units after the first post-fire growing season to measure crown volume scorch, crown volume consumption, basal scorch, and ground char for ponderosa pine seedlings and saplings. Logistic regression was used to model the probability of mortality based on tree size, flame length, and direct fire effects. Tree size, flame length, crown damage, ground char, and basal char severity were all important factors in the prediction of mortality. Observed mortality was >70% for seedlings but was only 18 to 46% for sapling-sized trees. The differences in mortality thresholds for ponderosa pine seedlings and saplings highlight their susceptibility to different damage pathways and give managers several options when designing burn prescriptions.