Cleavage of DNA into oligonucleosomal fragments, recognizable as a DNA ladder on agarose gel electrophoresis, is usually considered as the biochemical hallmark of apoptosis. Recently, it has been shown that this internucleosomal cleavage is preceded by the formation of large fragments of DNA of > or = 700, 200-250, and 30-50 kilobase pairs (kbp) in length. Using isolated thymocyte nuclei, we now demonstrate that the formation of these large fragments is Mg(2+)- but not Ca(2+)-dependent. Further degradation of > or = 460- and 200-250-kbp fragments to 30-50-kbp fragments but not oligonucleosomal cleavage is also Mg(2+)-dependent but is facilitated by Ca2+. In contrast, formation of oligonucleosomal fragments does not occur in the presence of either Ca2+ or Mg2+ alone but requires the presence of both cations. These results support the hypothesis that the formation of these large fragments and the subsequent internucleosomal cleavage are distinct steps in the degradation of DNA in apoptosis in thymocytes.