Transport of DNA across bacterial membranes during natural transformation is a fascinating and elaborate process. It requires the functional integrity of huge multi-protein complexes present in the bacterial envelope at distinct loci. After successful mapping of essential gene products involved in natural transformation, current research focuses on the functional interplay of these components in order to understand the mechanisms how DNA enters the bacterium. Here, we discuss the model of a two-step DNA uptake process in competent Gram-negative and Gram-positive bacteria. The first step comprises the transfer of DNA from the bacterial surface to the cytoplasmic membrane. For this purpose, bacteria use a variety of machineries, mostly, but not necessarily, sharing key homologous components. The second step is the translocation of DNA across the cytoplasmic membrane, a tight barrier at which ion gradients are established for energization of the cell. Crossing the latter is mediated by a protein complex harbouring a highly conserved membrane channel. On the basis of current data, at least the first step is uncoupled from the second. This review intends to highlight mechanistic features of both steps of bacterial DNA uptake by the integrative interpretation of genetic, biochemical and biophysical data.