Reduced impact logging (RIL) has been promoted as a cornerstone in sustainable forest management in the tropics, although the ecological implications of RIL guidelines are poorly understood. This study aims to identify the impact of RIL on the regeneration of commercial timber species by comparing the regeneration dynamics of logging gaps with naturally occuring canopy gaps. In the concession of Consorcio Forestal Amazonico in the region of Ucayali in the Peruvian Amazon, a total of 210 circular sample plots were established in 35 gaps in unmanaged natural forest and 35 canopy gaps in forest managed according to RIL guidelines. The size of each canopy gap was estimated by establishing a polygon that followed the vertical projection of the edge of the gap. Three circular plots of 100 m2 were established within each canopy gap. The center points of the plots were placed at the stump, mid-trunk and crown of the fallen tree. It appeared that the total abundance of seedlings did not differ significantly between logging gaps and natural canopy gaps. Instead the response to logging varied between species groups. The Clarisia sp. species group had a significant negative response to logging, while Ormosia sp., Aniba sp., Ocotea sp., Qualea sp. and Terminalia sp. were significantly more abundant in gaps of logged-over forest. A direct effect of seed tree retention on seedling abundance could not be detected statistically. Possible reasons for observed differences between untouched and logged forest and consequences of observed patterns for long-term forest development and management were discussed. It was concluded that issuing and enforcing strict guidelines on sustainable forest management is no guarantee for preserving species composition in tropical forests. © 2013 Elsevier B.V.