The response of the bilayer structure and dynamics to different types of inclusions is investigated using X-ray scattering techniques and the evidence is used to deduce details of their interaction with the membrane. In the case of the antimicrobial peptide RTD-1 we identify, combining the outcome of oriented CD spectroscopy and X-ray diffraction experiments, two different bound states of the peptide that differ in the orientation with respect to the membrane. One of which is shown by lamellar X-rays diffraction to considerably thin the membrane, while the other does not affect the membrane thickness. From this we identify the thinning state to be a surface state in which the peptide is embedded in the headgroup region of the bilayer. Furthermore we investigate the effect of small membrane-spanning helical peptides of different lengths on the bilayer using lamellar diffraction. Contrary to our expectations we did not measure any significant change in membrane thickness upon inclusion of these helices, which leads us review our idea of hydrophobic matching in the case of small single transmembrane peptides. In addition we used inelastic X-ray scattering at high energy resolution to investigate the collective chain dynamics of the membrane and how it is affected by inclusions in the membrane. We measure the inelastic X-ray scattering of DMPC bilayers with and without cholesterol. An analysis of these spectra within a generalized hydrodynamic theory yields the dispersion relation and damping of the high frequency sound modes. We show that this dispersion relation systematically changes with the amount of cholesterol in the sample. Comparing this finding with the situation in the pure lipid above and below the main phase transition we show that under the influence of the cholesterol the dynamics of the lipid becomes more gel-like, a fact that might have important implications for the transport of small molecules across the bilayer.