The small-scale structure of dark matter provides an important window into both physical properties of dark matter, and the primordial density fluctuations. In particular, deviations from the standard LCDM cosmological model can significantly impact the formation and evolution of dark matter structures, leading to observational differences in galaxy properties. In this talk, I will explore how such deviations influence observations of the Milky Way's satellite galaxies. Using a combination of numerical and analytical techniques, I will discuss the modelling of dark matter subhalos and their galaxies. Finally, I will discuss how galaxy properties constrain the primordial fluctuations and provide insights into specific dark matter models.