The cytolethal distending toxin B (CdtB) of the mouse pathogen Helicobacter hepaticus has cation binding and DNA catalysis residues in common with members of the mammalian deoxyribonuclease I (DNase I) family. The purpose of the present study was to characterize CdtB nuclease. To establish optimal digestion conditions and to evaluate co-factor requirements, a novel and sensitive fluorometric assay that quantitatively determines double stranded DNA digestion was developed. Although the Ca2+- and Mg2+-dependence and neutral properties of CdtB were similar to DNase I, hydrolysis of DNA by CdtB was approximately 100-fold less active than DNase I and was considerably more resistant to inhibition by ZnCl2 and G-actin.