We have carried out atomistic molecular dynamics simulations of C-60 fullerenes inside a dimyristoylphosphatidylcholine lipid bilayer and an alkane melt. Simulations reveal that the preferred position of a single C-60 fullerene is about 6-7 angstrom off of the center plane, allowing the fullerene to take advantage of strong dispersion interactions with denser regions of the bilayer. Further displacement (> 8 A) of the fullerene away from the center plane results in a rapid increase in free energy likely due to distortion of the lipid head group layer. The effective interaction between fullerenes (direct interaction plus environment (bilayer)-induced interaction), measured as the potential of mean force (POMF) between two fullerenes as a function of their separation, was found to be significantly less attractive in the lipid bilayer than in an alkane melt of the same molecular weight as the lipid tails. Only part of this difference can be accounted for by the more favorable interaction of the fullerene with the relatively denser bilayer. Additionally, our POMF studies indicate that the bilayer is less able to accommodate the larger aggregated fullerene pair than isolated single fullerenes, again likely due to distortion of the bilayer structure. The implications of these effects on aggregation of fullerenes within lipid bilayer are considered.