The propagation of cosmological ionisation fronts (I-fronts) during reionisation is strongly influenced by small-scale structure. Here we summarise our recent attempts to understand the effect of this small-scale structure. We present high resolution cosmological N-body simulations at high-z ($z>6$) which resolve a wide range of halo mass, from mini-halos to clusters of large, rare halos. We also study how mini-halos affect I-fronts, through simulations of mini-halo photo-evaporation including numerical gas dynamics with radiative transfer. Furthermore, we modify the I-front propagation equations to account for evolving small-scale structure, and incorporate these results into a semi-analytical reionisation model. When intergalactic medium clumping and mini-halo clustering around sources are included, small-scale structure affects reionisation by slowing it down and extending it in time. This helps to explain the observations of the Wilkinson Microwave Anisotropy Probe, which imply an early and extended reionisation epoch. We also study how source clustering affects the evolution and size of H II regions, finding, in agreement with simulations, that H II regions usually expand, and rarely shrink. Hence, “relic H II regions” are an exception, rather than the rule. When the suppression of small-mass sources in already-ionised regions by Jeans-mass filtering is accounted for, H II regions are smaller, delaying overlap. We also present a new numerical method for radiative transfer which is fast, efficient and easily coupled to hydrodynamics and N-body codes, along with sample tests and applications.