The subcellular distribution of both muscle and common type acylphosphatases was studied during apoptosis. Both isoenzymes were previously shown to have in vitro nucleolytic activity having a pH optimum at 6.8. In this paper we demonstrate a nuclear migration of the muscle type isoenzyme in response to various apoptotic stimuli either in K562 or in Jurkat cells, while the common type acylphosphatase isoform remains cytoplasmatic under the same conditions. Furthermore, we present evidences of a direct in vivo interaction between muscle acylphosphatase and two other DNAses of about 60 and 80 kDa in size. Our results are consistent with an in vivo involvement of the muscle isoform in apoptosis, possibly as a part of a multimeric protein complex that binds and hydrolyses DNA during this process.