The degradation of DNA into a specific pattern of fragments is a characteristic feature of apoptosis. Initially, these fragments were visualized by conventional agarose gel electrophoresis as a DNA ladder consisting of multimers of approximately 200 base pairs. Subsequent analysis by pulsed-field gel electrophoresis showed that there were also fragments in the 50- to 300-kilobase range. These size classes of DNA are generated by endonuclease activity at internucleosomal, interloop, and interrosette sites in chromatin and are, therefore, specifically related to the structural organization of chromatin in the nucleus. We have recreated this pattern of degradation in isolated nuclei and established the specific cation requirements for each stage. A model of chromatin degradation in apoptosis is described that incorporates all of the known cation, enzymatic, and structural aspects of the process.Key words: apoptosis, endonuclease, chromatin, calcium, nucleus.