In this paper we report on the structural analysis of bilayers of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) using polarization modulation infrared reflection absorption spectroscopy (PM IRRAS). The lipid bilayers were formed on SiO2|Au and Au surfaces using the Langmuir-Blodgett and Langmuir-Schaeffer techniques. As we showed in part 1 (Zawisza, I.; Wittstock, G.; Boukherroub, R.; Szunertis, S. Langmuir 2007, 23, 9303-9309), SiO2 layers of 7 nm thickness, synthesized by plasma-enhanced chemical vapor deposition on 200 nm thick gold covered glass slides, allow PM IRRAS investigations. Only minor changes in the order and structure of the lipid bilayer are observed when deposited on SiO2|Au and Au surfaces. The choline moiety in the leaflet directed toward the SiO2 surface exists in trans conformation and shows a tilt of 28 degrees with the surface normal of the CN bond. On the silica surface in the second leaflet directed toward air and in two layers deposited on the Au surface, trans and gauche isomers of the choline moiety are present and the tilt of the CN bond increases to 55 degrees with respect to the surface normal. The order and molecular orientation in the DMPC bilayers on SiO2 and Au surfaces are not affected by time. The analysis of the phosphate stretching mode on the Au surface shows slight dehydration of this group and reorientation of the phosphate moiety.