By using Aevol, a simulation framework designed to study the evolution of genome structure, we investigate the effect of homologous rearrangements on the course of evolution. We designed an efficient model of rearrangements based on an intermittent search algorithm. Then, using experimental in silico evolution, we explore the effect of rearrangement rates on the genome structure. We show that the effect of homologous rearrangements is quite complex. At first glance they appear to be dangerous enough to trigger an indirect selective pressure leading to short genomes when the rearrangement rate is high. However, by analyzing the successful lineage in the best runs, we found that there is a positive correlation between the number of homologous rearrangements and the fitness improvement in these lineages. Thus the impact of homologous rearrangements on evolution is rather complex: dangerous on the one hand but necessary on the other hand, to ensure a sufficient level of evolvability to the organisms. Moreover, our results show that the spontaneous rate of small mutations influences the relative proportions of homologous versus nonhomologous rearrangements.