The presented paper analyses deer impact on tree species and height diversity of young trees in three localities of the Czech Republic. The selected localities consisted of one fenced part, where deer has been excluded for a long time; and an unfenced part with free access to deer. The data were collected within the framework of the statistical forest inventory based on systematic sampling of the inventoried area. Tree species and height diversity were quantified using ten diversity indices. The analysis revealed that excessive deer densities pose a threat both to tree species and height diversity of young trees. Higher negative deer impact on tree species diversity can be expected on acidic sites, while height diversity is more sensitive to deer influence on fertile sites. However, if deer densities are low and do not reach the carrying capacity of the site, deer presence has no effect on tree species and height diversity of young trees.