Abrupt changes in site conditions due to windthrow initiate altered dynamics in humus formation, which affect germination, seedling growth and rooting patterns and thus also reforestation. This study examines changes in the upper soil horizons of four long-term observation sites with regard to morphology (humus form), porosity and rooting patterns. The new tall vegetation produces a different type and amount of litter, and the microclimate near the soil surface changes. Biological activity, organic matter turnover and mixing with the mineral fraction are accelerated. Where clearing operations damaged the soil, increased soil density and clogging of pores in the rooting zone impair drainage and aeration, which hinders rooting patterns and retards resettlement by trees, so that reforestation is greatly delayed. Clearing operations should cause as little damage as possible and new stock should be appropriate to the site type.