The objective of the EU Habitat Directive and the Natura 2000 site program is to conserve biological diversity through conservation of natural habitats. In line with this objective, conservation of the structural diversity of habitats, including deadwood and tree microhabitats, is crucial. In all EU countries the volume or number of dead trees and the number of “habitat trees” is taken into account in assessing habitat conservation status, although the details and threshold values vary between countries. A lack of those features, and too-low thresholds for them, may lead to ineffective implementation of a Natura 2000; this means that even a forest that has a favourable conservation status may not maintain or restore the biodiversity of its habitats. In the Polish system of natural habitats monitoring, the total volume of deadwood and coarse woody debris is surveyed. In some types of forest habitats the number of trees providing microhabitats is also recorded. The objective of increasing deadwood and habitat tree resources is taken into account in drafting Natura 2000 site management plans, but measures consisting only of leaving deadwood and habitat trees seem insufficient. The opportunities offered by occasional disturbances should be seized, and some trees should be allowed to age and die so that they provide particular microhabitat structures.