To study the effect of fluorination of the core of a phospholipid bilayer we performed two molecular dynamics computer simulations. The first simulation was performed on a regular dimyristoylphosphatidylcholine (DMPC) bilayer, the second simulation was performed on its fluorinated counterpart FDMPC. In FDMPC, bilayer hydrogen atoms belonging to the last four hydrocarbon groups in both chains of phospholipid molecules were replaced by fluorines. From our simulations we observed that as a result of fluorination the core of the bilayer represented a tightly packed structure, while the structure of the head groups and of the region in the beginning of the tails remained similar to the one observed in the ordinary bilayer. A simple model for charge distribution in the phospholipid tails was proposed which explained the change in the sign of the dipole potential due to fluorination.