Classical thermodynamics is a theory for a collection of molecules in equilibrium. What happens if the number of molecules in the system becomes smaller and smaller, and the system boundaries reflect conditions further and further away from equilibrium? Can we still use thermodynamics? This lecture aims to explain that the field of non-equilibrium thermodynamics can be extended to describe in a systematic manner even molecular behaviour far from equilibrium conditions. We start introducing the concept of internal variables, derive the law of mass action, and end illustrating the theory by applications to RNA stretching experiments and active transport by the Ca-ATPase. We discuss that a thermodynamic theory is needed, also for molecules. References S. Kjelstrup, D. Bedeaux, Isabella Inzoli, Jean-Marc Simon, Criteria for validity of thermodynamic equations from non-equilibrium molecular dynamics simulations, Energy, 33 (2008) 1185-1196 J.M. Rubi, D. Bedeaux and S. Kjelstrup, Thermodynamics for small molecule stretching experiments, J. Phys. Chem. B, 110 (2006) 12733-12737 D. Bedeaux and S. Kjelstrup, The measurable heat flux that accompanies active transport by the Ca- ATPase. Phys. Chem. Chem. Phys. 48 (2008) 7304-7317.