American beech (Fagus grandifolia Ehrh.) regenerates both from seed and also clonally via root sprouts. Regenerating beech saplings often form dense and depauperate understories that cast deep shade and displace co-occurring species. The relative proportion of saplings that originate from seed versus root sprouts varies widely throughout the range of beech. Although the cause for that variation remains unclear, it may be linked to canopy or soil disturbances, the spread of beech bark disease (BBD), or overabundant deer. Here, we asked whether the long-term exclusion of deer and the absence of BBD would favor the regeneration of saplings (20–150 cm tall) of seed origin versus those of sprout origin. We addressed this question using deer exclosures (16 and 60 yr old) and paired controls in one forest in Pennsylvania where BBD had caused major adult mortality and another where BBD was not present. We found that excluding deer significantly decreased the relative proportion of root sprouts from approximately 60% to approximately 25% in each forest, regardless of stand age, exclosure age, soil type, and presence or absence of BBD. Our findings provide evidence that deer, acting as herbivores, seed predators, agents of physical disturbance, or all of those simultaneously, create forest understories where root sprouts predominate. Although speculative, our results may apply to large regions because deer have been overabundant throughout much of the geographic range of American beech.