The transfer of various nano-scale fullerenes into lipid bilayers has been studied using all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations. The free energy change, when C-60, C-180, and C-540 fullerenes are transferred from water to the interior of a lipid [dioleoylphosphatidylcholine (DOPC)] bilayer, has been calculated. Upon entering the lipid bilayer, the largest (2.4 nm diameter) fullerene causes local distortions in the bilayer surface, which were previously observed in carbon nanotube simulations. These local distortions, however, do not lead to any free energy barriers to bilayer entry. The free energy profiles confirm spontaneous absorption of all three fullerenes. Qualitative agreement was observed when comparing fullerene partitioning in water/bilayer systems to water-hexane systems. In contrast to these nonspecific single fullerene properties, extensive CG-MD simulations of fullerene rich lipid bilayers reveal substantial impact of fullerene-size on the bilayer stability. While previous CG-MD simulations indicated that bilayer bound C-60 aggregates have little effect on the bilayer structure, the present MD simulations indicate that C-540 aggregation has drastic effects. Specifically, the observed destabilization likely has implications for understanding the cytotoxic mechanisms of nano-carbon particles upon uptake by biological cells.