Based on the theory of stellar structure and evolution combined with the theory of stellar atmospheres theoretical properties of young stars can be calculated. These calculations of pre-main sequence evolution have been refined over the last decades and do now provide theoretical spectra and colours even for very cool objects like young stars brown dwarfs and planets. Two of their key assumptions must become invalid towards the formation phases: (1) the hydrostatic equilibrium of pressure forces and gravity that assumes stellar matter to be at rest and (2) the non-dependence on the initial thermal structure. The former (1) is violated by accretion- and collapse flows, the latter (2) because a new born young star is observed with the specific thermal structure produced by the cloud collapse. I discuss changes in the theoretical properties of young stars that follow from calculating the pre-main sequence evolution as the consequence of the collapse of Bonnor-Ebert spheres.