Lipid bilayers form the basic structure of cellular membranes creating a semi-permeable barrier necessary for separating distinct chemical environments. Hydrophilic pores can form in bilayers that breach the barrier potentially causing cell death or enhance the uptake of hydrophilic molecules. We use molecular dynamics simulations and free energy calculations to investigate pore formation in model bilayers. The free energy barrier for pore formation is much lower in thinner phosphatidylcholine bilayers compared to thicker bilayers. The free energy barrier is due to an unfavourable change in entropy while the enthalpy of pore formation is favourable. These results have implications on a wide range of biological and biotechnological applications such as drug delivery antimicrobial peptides and transmembrane structure and stability.