Mechanical site preparation (MSP) is often performed prior to planting to improve the growth and survival of planted seedlings. In this study, we compared root development of 5-years-old Quercus petraea and Pinus nigra seedlings planted in plots that had been prepared with different methods, i.e. deep scarification, deep scarification combined with mounding-subsoiling, herbicide and a control without preparation. Seventy-two trees were excavated (36 per species) and their root system was measured by recording points in a three-dimensional space along their roots. The variation of the number of roots with depth and distance to root collar was assessed and analysed, as well as the root projection area. Our results showed that root development was better in the plots with mechanical preparation, for both Q. petraea and P. nigra, when compared to the control. Combining mounding to subsoiling made the roots extending deeper, especially for Q. petraea. A strong relationship was found between root projection area and root collar diameter, indicating the primary effect of lateral root spread on tree growth. The herbicide treatment induced the highest root growth, which raised questions about the potential negative effects of changes in soil properties caused by MSP methods.