We have developed a novel method for in vivo evaluation of cell death in patients with acute and/or chronic heart diseases, which are accompanied by apoptosis or cell necrosis. The method is based on the analysis of cell free DNA (cfDNA) in the blood serum (or plasma). The major parameters assessed in the method include total concentration of serum cfDNA, concentration of serum ribosomal repeat (rDNA), content of rDNA in total cfDNA, as well as factors of cfDNA elimination, such as nuclease activity and anti-DNA antibody. We demonstrated a fivefold increase in the serum cfDNA concentration and a 12-fold enhancement of serum rDNA concentration in patients with acute myocardial infarction compared with healthy individuals. In chronic coronary ischemia the serum cfDNA concentration was similar to that in the disease-free group. However, the content of rDNA in cfDNA was 4.8-fold higher, and the serum rDNA concentration was increased sevenfold. We hypothesize that one reason for accumulation of rDNA within cfDNA might be the previously reported resistance of rDNA to the ds-fragmentation by serum endonucleases. In both acute and chronic coronary disease the nuclease activity in the serum was substantially higher than that in the healthy cohort. Moreover, the titer of anti-DNA antibodies was elevated, with these antibodies being mostly bound to the cfDNA. Thus, the release of rDNA fragments into the blood not only reflects cellular death in the body but also determines the response of the organism to the disease-associated stress.