In bacteria, the chromosome is folded into a structure called the nucleoid. This compaction must facilitate and maintain key biological processes such as gene expression and DNA transactions (replication, recombination, repair, segregation). Chromosome and chromatin 3D-organization in bacteria has been a puzzle for decades. Chromosome conformation capture coupled to deep sequencing (HiC) in combination with other ‘omics’ approaches has allowed dissection of the structural layers that shape bacterial chromosome organization, from DNA topology to global chromosome architecture. Here we review the latest findings in the field and discuss the main features of bacterial genome folding.