There is a fundamental connection between the class of diffusions in natural scale, and a certain class of solutions to the Skorokhod Embedding Problem (SEP). We show that the important concept of minimality in the SEP leads to the new and useful concept of a minimal diffusion. Minimality is closely related to the martingale property. A diffusion is minimal if it minimises the expected local time at every point among all diffusions with a given distribution at an exponential time. Our approach makes explicit the connection between the boundary behaviour, the martingale property and the local time characteristics of time-homogeneous diffusions.