The cell membrane acts as a physical barrier that separates the biological machinery of life from a potentially hostile external environment. The cell membrane itself is composed of two major components: a phospholipid bilayer that acts as a physical barrier, limiting the passive diffusion of compounds into the cell interior; and membrane proteins, which selectively control the traffic of drugs, ions and other compounds into or out of the cell. Disorders in membrane transport processes underpin a vast array of conditions, ranging from antibiotic resistance to cystic fibrosis. However, neither the diffusive permeation of molecules through the cell membrane, nor their active transport by membrane transport proteins has been fully characterised at a molecular level. Here I will discuss the factors influencing the diffusive uptake and transporter-mediated efflux of drug substrates from a structural and molecular dynamics perspective. In particular, the influence of crystallisation conditions on the conformation and structural dynamics of a multidrug transporter; the energetics governing the binding and transport of drug substrates; and the effect of cholesterol on the partitioning of drugs into the membrane will be discussed.