The present study analyzes the staining pattern of DNA in situ end-labeling techniques of human and rabbit atherosclerotic plaques. Both the terminal deoxynucleotidyl transferase end-labeling and the in situ nick translation technique detected, besides apoptotic nuclei, numerous round vesicles with diameters from 0.5 to 5 microns within the atherosclerotic plaques. These vesicles did not contain DNA but contained calcium. A pretreatment with EDTA or citric acid abolished the labeling of the vesicles but did not influence the detection of apoptotic nuclei. Ultrastructurally, the vesicles were of variable diameter and density, and their aspect was compatible with matrix vesicles, which are well known in epiphyses during bone formation. The larger vesicles contained cell organelles, and the small vesicles were very dense. X-ray microanalysis demonstrated high calcium and phosphorus levels within the most dense vesicles. Different stages of the process were present in the plaques. In this way we could demonstrate that cytoplasmic fragmentation of smooth muscle cells and subsequent formation of matrix vesicles are a frequent finding in atherosclerotic plaques. The association of apoptotic cell death and formation of matrix vesicles could be an interesting pathway in explaining calcification of atherosclerotic plaques. Both the terminal deoxynucleotidyl transferase end-labeling and the in situ nick translation technique detected simultaneously apoptotic nuclei and matrix vesicles if calcium is not removed from the sections.