Molecular dynamics simulations were used to study the effect of periodic roughness of PE and PVC polymer surfaces on the hydrophobicity. Pillars of different lateral dimensions and heights were derived from flat crystalline surfaces, and the results of nanoscale simulations on the structured surfaces were compared with theoretical predictions of the Wenzel and Cassie equations. Hydrophobicity increased on all rough surfaces, but the increase was greater on the structured PE surfaces because of the larger water contact angle on the flat PE surface than the corresponding PVC surface. Equally sized pillar structures on the two polymers resulted in different equilibrium wetting geometries. Composite contacts were observed on rough PE surfaces, and the contact angle increased with decreasing contact area between the solid and the liquid. Opposite results were obtained for rough PVC surfaces; the contact angle increased with the solid-liquid contact area, in agreement with Wenzel's equation. However, the composite contact was observed if the energies of the wetted and composite contacts were almost equal. Good agreement was obtained between the simulated contact angles and equilibrium droplet shapes and the theories but there were also some limitations of the nanoscale simulations.