Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences with remarkable specificity. Type II REases are highly divergent in sequence as well as in topology, i.e. the connectivity of secondary structure elements. A widely held assumption is that a structural core of five beta-strands flanked by two alpha-helices is common to these enzymes. We introduce a systematic procedure to enumerate secondary structure elements in an unambiguous and reproducible way, and use it to analyze the currently available X-ray structures of Type II REases. Based on this analysis, we propose an alternative definition of the core, which we term the alphabetaalpha-core. The alphabetaalpha-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand beta-sheet and two alpha-helices on the same face of the beta-sheet. We use the alphabetaalpha-core connectivity as a basis for grouping the Type II REases into distinct structural classes. In these new structural classes, the connectivity correlates with the angles between the secondary structure elements and with the cleavage patterns of the REases. We show that there exists a substructure of the alphabetaalpha-core, namely a common conserved core, ccc, defined here as one alpha-helix and four beta-strands common to all Type II REase of known structure.