Spin polarized density functional theory was employed to investigate the influence of organic functional groups on the electronic properties of graphene nanoflakes (GNF). We found that for -OH functionalized GNF, energy gap decreases as the number of layers is increased regardless of the stacking pattern (ABA and AAA). In the case of -SH functionalized GNF the energy gap depends on the number of layers and on the stacking pattern. The observed trends were clarified in terms of interactions between pi-electron rich beds. Our results bring new insights into engineering the properties of GNFs by modification of their surface chemistry and stacking conformation. (C) 2010 Elsevier B. V. All rights reserved.