Bacterial chromosomes must be compacted by three-orders of magnitude to fit within the cell. While such compaction could in theory yield disordered structures, it is becoming increasingly clear that bacterial chromosomes are in fact arranged in regular and reproducible fashions and that their configurations are tightly connected to fundamental processes such as chromosome segregation. Nonetheless, due to throughput and resolution limitations associated with traditional assays, many question regarding bacterial chromosome structure and its relation to genome function remain. Here, I review the related technologies, chromosome conformation capture (3C) and chromosome conformation capture carbon copy (5C), which my collaborators and I recently introduced as tools to probe the high-resolution folding of entire bacterial genomes. These technologies utilize covalent cross-linking and proximity ligation to facilitate the measurement of the spatial positioning of hundreds of genomic loci, thereby opening the door to high-throughput studies of bacterial chromosome structure. Hence, 3C and 5C represent powerful new tools for assaying the three-dimensional architecture of bacterial genomes.