This paper aims at reviewing the ecological effects of windthrow and the processes by which the structure and composition of the boreal forest are affected. The windthrow problem has been investigated at different levels: landscape; forest community; and fallen tree ecosystem. All original data are from the natural, protected, uneven-aged boreal spruce forests of the central Russian Plain. Mapping of vegetation was used to detect windthrow processes in primary forest communities. The scales of windthrow gaps in space and time determine the patch structure of the forest ecosystems. The main result of this phenomenon is the occurrence of gap-phase dynamics in forest communities. The development of gaps is very important for the survival of small- and broad-leaved trees in boreal coniferous forests. In the case study of the scales of natural windthrow disturbances it was found that in uneven-aged spruce forests, 7–12% of the surface was covered by pit-and-mound topography. After widespread windthrow, this figure rised to 15–25%. In this context, a procedure for dating windthrow topography was developed, along with methods of diagnosing uprooting disturbances of the soil. Much attention was also paid to the structure and properties of soil where uprooting had occurred. It was found that the microsites which are found in pit-and-mound topography differ pedogenically. Furthermore, the nature and rate of recovery of the background soil profile after uprooting varied a lot, i.e. under the influence of shallow uprooting, the reconstruction of the background soil combination and processes was completed in 100–200 years. Where as in cases of major uprootings, it took more than a 200–300 year cycle. The role of tree uprooting in maintaining stable tree and grass population structures in forest communities was found very important. The spatial distribution of trees was associated with pit-and-mound topography in all types of forests. Furthermore, spruce regenerated better on mounds and fallen trees than on undisturbed surfaces. Multi-aged tree regrowth was therefore being constantly formed in virgin forests. There was also increase in the community floristic richness due to the establishment of certain pioneer species from other communities in microsites disturbed by uprooting. The gene pool of a population was rejuvenated as the plants appeared in these microsites from seeds and spores, while propagation in undisturbed areas was predominantly vegetative. As a result, the structure of forest plant populations was found to be in a stable multi-aged state.